Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 12:55:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/04_2023/7ub2_26434.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/04_2023/7ub2_26434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/04_2023/7ub2_26434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/04_2023/7ub2_26434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/04_2023/7ub2_26434.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/04_2023/7ub2_26434.pdb" } resolution = 3.4 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= 0.066 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: 5 Type Number sf(0) Gaussians P 98 5.49 5 S 70 5.16 5 C 11050 2.51 5 N 2933 2.21 5 O 3428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 17579 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1029 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "Z" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 980 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Time building chain proxies: 9.10, per 1000 atoms: 0.52 Number of scatterers: 17579 At special positions: 0 Unit cell: (106.981, 115.072, 166.315, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 98 15.00 O 3428 8.00 N 2933 7.00 C 11050 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: 7.33 Conformation dependent library (CDL) restraints added in 2.4 seconds 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 30 sheets defined 48.7% alpha, 21.5% beta 39 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 4.78 Creating SS restraints... Processing helix chain 'E' and resid 34 through 48 removed outlier: 3.580A pdb=" N LYS E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 62 removed outlier: 3.682A pdb=" N PHE E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 190 Processing helix chain 'E' and resid 193 through 199 removed outlier: 4.016A pdb=" N LYS E 198 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET E 203 " --> pdb=" O ASP E 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 48 removed outlier: 3.580A pdb=" N LYS F 48 " --> pdb=" O VAL F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.682A pdb=" N PHE F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 193 through 199 removed outlier: 4.016A pdb=" N LYS F 198 " --> pdb=" O PHE F 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP F 199 " --> pdb=" O GLY F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 217 removed outlier: 4.168A pdb=" N MET F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 48 removed outlier: 3.581A pdb=" N LYS G 48 " --> pdb=" O VAL G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 62 removed outlier: 3.681A pdb=" N PHE G 52 " --> pdb=" O LYS G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 190 Processing helix chain 'G' and resid 193 through 199 removed outlier: 4.015A pdb=" N LYS G 198 " --> pdb=" O PHE G 194 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP G 199 " --> pdb=" O GLY G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET G 203 " --> pdb=" O ASP G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 48 removed outlier: 3.581A pdb=" N LYS H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 62 removed outlier: 3.681A pdb=" N PHE H 52 " --> pdb=" O LYS H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL H 74 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 190 Processing helix chain 'H' and resid 193 through 199 removed outlier: 4.016A pdb=" N LYS H 198 " --> pdb=" O PHE H 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP H 199 " --> pdb=" O GLY H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 217 removed outlier: 4.170A pdb=" N MET H 203 " --> pdb=" O ASP H 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 48 removed outlier: 3.581A pdb=" N LYS I 48 " --> pdb=" O VAL I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 62 removed outlier: 3.682A pdb=" N PHE I 52 " --> pdb=" O LYS I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 121 removed outlier: 3.619A pdb=" N GLY I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 190 Processing helix chain 'I' and resid 193 through 199 removed outlier: 4.016A pdb=" N LYS I 198 " --> pdb=" O PHE I 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP I 199 " --> pdb=" O GLY I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET I 203 " --> pdb=" O ASP I 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 48 removed outlier: 3.580A pdb=" N LYS J 48 " --> pdb=" O VAL J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 62 removed outlier: 3.681A pdb=" N PHE J 52 " --> pdb=" O LYS J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 190 Processing helix chain 'J' and resid 193 through 199 removed outlier: 4.016A pdb=" N LYS J 198 " --> pdb=" O PHE J 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP J 199 " --> pdb=" O GLY J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET J 203 " --> pdb=" O ASP J 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 48 removed outlier: 3.581A pdb=" N LYS K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 62 removed outlier: 3.682A pdb=" N PHE K 52 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 121 removed outlier: 3.619A pdb=" N GLY K 121 " --> pdb=" O ALA K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 190 Processing helix chain 'K' and resid 193 through 199 removed outlier: 4.016A pdb=" N LYS K 198 " --> pdb=" O PHE K 194 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET K 203 " --> pdb=" O ASP K 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 48 removed outlier: 3.581A pdb=" N LYS L 48 " --> pdb=" O VAL L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 62 removed outlier: 3.681A pdb=" N PHE L 52 " --> pdb=" O LYS L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY L 121 " --> pdb=" O ALA L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 190 Processing helix chain 'L' and resid 193 through 199 removed outlier: 4.015A pdb=" N LYS L 198 " --> pdb=" O PHE L 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP L 199 " --> pdb=" O GLY L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET L 203 " --> pdb=" O ASP L 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 48 removed outlier: 3.581A pdb=" N LYS M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 62 removed outlier: 3.682A pdb=" N PHE M 52 " --> pdb=" O LYS M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL M 74 " --> pdb=" O ASP M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY M 121 " --> pdb=" O ALA M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 190 Processing helix chain 'M' and resid 193 through 199 removed outlier: 4.015A pdb=" N LYS M 198 " --> pdb=" O PHE M 194 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP M 199 " --> pdb=" O GLY M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET M 203 " --> pdb=" O ASP M 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 48 removed outlier: 3.580A pdb=" N LYS N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 62 removed outlier: 3.682A pdb=" N PHE N 52 " --> pdb=" O LYS N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 84 removed outlier: 3.514A pdb=" N VAL N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 121 removed outlier: 3.619A pdb=" N GLY N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 190 Processing helix chain 'N' and resid 193 through 199 removed outlier: 4.015A pdb=" N LYS N 198 " --> pdb=" O PHE N 194 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP N 199 " --> pdb=" O GLY N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET N 203 " --> pdb=" O ASP N 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 95 through 100 Processing sheet with id=AA2, first strand: chain 'E' and resid 123 through 132 Processing sheet with id=AA3, first strand: chain 'E' and resid 136 through 140 removed outlier: 7.189A pdb=" N GLU E 147 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP E 139 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU E 145 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 95 through 100 Processing sheet with id=AA5, first strand: chain 'F' and resid 123 through 132 Processing sheet with id=AA6, first strand: chain 'F' and resid 136 through 140 removed outlier: 7.188A pdb=" N GLU F 147 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TRP F 139 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU F 145 " --> pdb=" O TRP F 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 95 through 100 Processing sheet with id=AA8, first strand: chain 'G' and resid 123 through 132 Processing sheet with id=AA9, first strand: chain 'G' and resid 136 through 140 removed outlier: 7.188A pdb=" N GLU G 147 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TRP G 139 " --> pdb=" O GLU G 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU G 145 " --> pdb=" O TRP G 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 95 through 100 Processing sheet with id=AB2, first strand: chain 'H' and resid 123 through 132 Processing sheet with id=AB3, first strand: chain 'H' and resid 136 through 140 removed outlier: 7.188A pdb=" N GLU H 147 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP H 139 " --> pdb=" O GLU H 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU H 145 " --> pdb=" O TRP H 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 95 through 100 Processing sheet with id=AB5, first strand: chain 'I' and resid 123 through 132 Processing sheet with id=AB6, first strand: chain 'I' and resid 136 through 140 removed outlier: 7.188A pdb=" N GLU I 147 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP I 139 " --> pdb=" O GLU I 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU I 145 " --> pdb=" O TRP I 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 95 through 100 Processing sheet with id=AB8, first strand: chain 'J' and resid 123 through 132 Processing sheet with id=AB9, first strand: chain 'J' and resid 136 through 140 removed outlier: 7.187A pdb=" N GLU J 147 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP J 139 " --> pdb=" O GLU J 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU J 145 " --> pdb=" O TRP J 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 95 through 100 Processing sheet with id=AC2, first strand: chain 'K' and resid 123 through 132 Processing sheet with id=AC3, first strand: chain 'K' and resid 136 through 140 removed outlier: 7.188A pdb=" N GLU K 147 " --> pdb=" O LEU K 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP K 139 " --> pdb=" O GLU K 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU K 145 " --> pdb=" O TRP K 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 95 through 100 Processing sheet with id=AC5, first strand: chain 'L' and resid 123 through 132 Processing sheet with id=AC6, first strand: chain 'L' and resid 136 through 140 removed outlier: 7.187A pdb=" N GLU L 147 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TRP L 139 " --> pdb=" O GLU L 145 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU L 145 " --> pdb=" O TRP L 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 95 through 100 Processing sheet with id=AC8, first strand: chain 'M' and resid 123 through 132 Processing sheet with id=AC9, first strand: chain 'M' and resid 136 through 140 removed outlier: 7.187A pdb=" N GLU M 147 " --> pdb=" O LEU M 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP M 139 " --> pdb=" O GLU M 145 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU M 145 " --> pdb=" O TRP M 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 95 through 100 Processing sheet with id=AD2, first strand: chain 'N' and resid 123 through 132 Processing sheet with id=AD3, first strand: chain 'N' and resid 136 through 140 removed outlier: 7.187A pdb=" N GLU N 147 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP N 139 " --> pdb=" O GLU N 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU N 145 " --> pdb=" O TRP N 139 " (cutoff:3.500A) 791 hydrogen bonds defined for protein. 2343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 5.18 Time building geometry restraints manager: 7.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4337 1.33 - 1.45: 3840 1.45 - 1.57: 9651 1.57 - 1.69: 194 1.69 - 1.81: 130 Bond restraints: 18152 Sorted by residual: bond pdb=" CB LYS K 68 " pdb=" CG LYS K 68 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CB LYS G 68 " pdb=" CG LYS G 68 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CB LYS F 68 " pdb=" CG LYS F 68 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CB LYS H 68 " pdb=" CG LYS H 68 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CB LYS M 68 " pdb=" CG LYS M 68 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.01e+00 ... (remaining 18147 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.50: 857 106.50 - 113.37: 9666 113.37 - 120.24: 6601 120.24 - 127.11: 7381 127.11 - 133.98: 396 Bond angle restraints: 24901 Sorted by residual: angle pdb=" N ILE I 88 " pdb=" CA ILE I 88 " pdb=" C ILE I 88 " ideal model delta sigma weight residual 112.17 108.26 3.91 9.50e-01 1.11e+00 1.69e+01 angle pdb=" N ILE N 88 " pdb=" CA ILE N 88 " pdb=" C ILE N 88 " ideal model delta sigma weight residual 112.17 108.27 3.90 9.50e-01 1.11e+00 1.69e+01 angle pdb=" N ILE G 88 " pdb=" CA ILE G 88 " pdb=" C ILE G 88 " ideal model delta sigma weight residual 112.17 108.28 3.89 9.50e-01 1.11e+00 1.68e+01 angle pdb=" N ILE K 88 " pdb=" CA ILE K 88 " pdb=" C ILE K 88 " ideal model delta sigma weight residual 112.17 108.28 3.89 9.50e-01 1.11e+00 1.68e+01 angle pdb=" N ILE M 88 " pdb=" CA ILE M 88 " pdb=" C ILE M 88 " ideal model delta sigma weight residual 112.17 108.28 3.89 9.50e-01 1.11e+00 1.67e+01 ... (remaining 24896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8242 17.99 - 35.97: 1654 35.97 - 53.96: 421 53.96 - 71.95: 190 71.95 - 89.94: 27 Dihedral angle restraints: 10534 sinusoidal: 4944 harmonic: 5590 Sorted by residual: dihedral pdb=" CA ASP F 201 " pdb=" CB ASP F 201 " pdb=" CG ASP F 201 " pdb=" OD1 ASP F 201 " ideal model delta sinusoidal sigma weight residual -30.00 -86.59 56.59 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP N 201 " pdb=" CB ASP N 201 " pdb=" CG ASP N 201 " pdb=" OD1 ASP N 201 " ideal model delta sinusoidal sigma weight residual -30.00 -86.56 56.56 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP L 201 " pdb=" CB ASP L 201 " pdb=" CG ASP L 201 " pdb=" OD1 ASP L 201 " ideal model delta sinusoidal sigma weight residual -30.00 -86.55 56.55 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 10531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1785 0.029 - 0.057: 634 0.057 - 0.086: 187 0.086 - 0.115: 97 0.115 - 0.143: 19 Chirality restraints: 2722 Sorted by residual: chirality pdb=" CA ILE H 126 " pdb=" N ILE H 126 " pdb=" C ILE H 126 " pdb=" CB ILE H 126 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE K 126 " pdb=" N ILE K 126 " pdb=" C ILE K 126 " pdb=" CB ILE K 126 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE F 126 " pdb=" N ILE F 126 " pdb=" C ILE F 126 " pdb=" CB ILE F 126 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 2719 not shown) Planarity restraints: 2758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE N 88 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C ILE N 88 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE N 88 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP N 89 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 88 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.48e+00 pdb=" C ILE J 88 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE J 88 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP J 89 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 88 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C ILE G 88 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE G 88 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP G 89 " -0.011 2.00e-02 2.50e+03 ... (remaining 2755 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 443 2.69 - 3.24: 15014 3.24 - 3.79: 24873 3.79 - 4.35: 32653 4.35 - 4.90: 56899 Nonbonded interactions: 129882 Sorted by model distance: nonbonded pdb=" NE2 GLN N 107 " pdb=" N7 DA Y 67 " model vdw 2.134 2.600 nonbonded pdb=" NE2 GLN H 107 " pdb=" N7 DA Y 37 " model vdw 2.145 2.600 nonbonded pdb=" NE2 GLN I 107 " pdb=" N7 DA Y 42 " model vdw 2.173 2.600 nonbonded pdb=" NE2 GLN M 107 " pdb=" N7 DA Y 62 " model vdw 2.181 2.600 nonbonded pdb=" NE2 GLN J 107 " pdb=" N7 DA Y 47 " model vdw 2.211 2.600 ... (remaining 129877 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 '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' } 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.410 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 48.980 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.003 0.043 18152 Z= 0.162 Angle : 0.563 9.129 24901 Z= 0.324 Chirality : 0.037 0.143 2722 Planarity : 0.002 0.019 2758 Dihedral : 20.861 89.936 6954 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer Outliers : 0.60 % 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: 0.65 (0.19), residues: 1890 helix: 2.71 (0.18), residues: 850 sheet: -0.50 (0.25), residues: 350 loop : -2.13 (0.19), residues: 690 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 384 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 390 average time/residue: 0.3180 time to fit residues: 180.9065 Evaluate side-chains 339 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 335 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1563 time to fit residues: 3.8788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 101 optimal weight: 0.0770 chunk 80 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN I 61 ASN L 187 GLN N 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 18152 Z= 0.211 Angle : 0.566 7.345 24901 Z= 0.317 Chirality : 0.041 0.184 2722 Planarity : 0.003 0.026 2758 Dihedral : 19.455 89.723 3054 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 3.05 % 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: 0.79 (0.19), residues: 1890 helix: 2.84 (0.17), residues: 850 sheet: -0.47 (0.25), residues: 350 loop : -2.04 (0.20), residues: 690 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 313 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 29 residues processed: 345 average time/residue: 0.3250 time to fit residues: 166.1832 Evaluate side-chains 328 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 299 time to evaluate : 1.960 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1907 time to fit residues: 12.3592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN G 61 ASN I 61 ASN I 169 ASN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 18152 Z= 0.269 Angle : 0.594 8.175 24901 Z= 0.332 Chirality : 0.042 0.197 2722 Planarity : 0.003 0.028 2758 Dihedral : 19.562 89.649 3054 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 2.87 % 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: 0.54 (0.19), residues: 1890 helix: 2.48 (0.17), residues: 870 sheet: -0.47 (0.26), residues: 350 loop : -2.17 (0.20), residues: 670 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 309 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 22 residues processed: 331 average time/residue: 0.3320 time to fit residues: 159.0161 Evaluate side-chains 326 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 304 time to evaluate : 1.859 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1770 time to fit residues: 9.4620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN F 107 GLN G 61 ASN K 61 ASN K 187 GLN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 18152 Z= 0.183 Angle : 0.540 7.119 24901 Z= 0.306 Chirality : 0.040 0.200 2722 Planarity : 0.003 0.026 2758 Dihedral : 19.558 89.205 3054 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 1890 helix: 2.52 (0.17), residues: 870 sheet: -0.43 (0.26), residues: 350 loop : -2.25 (0.19), residues: 670 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 309 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 22 residues processed: 331 average time/residue: 0.3284 time to fit residues: 158.3749 Evaluate side-chains 318 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 296 time to evaluate : 1.973 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2225 time to fit residues: 10.6127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 97 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN G 61 ASN H 140 ASN I 61 ASN K 67 GLN K 187 GLN L 187 GLN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 18152 Z= 0.224 Angle : 0.562 7.862 24901 Z= 0.317 Chirality : 0.041 0.174 2722 Planarity : 0.003 0.027 2758 Dihedral : 19.522 89.163 3054 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 1890 helix: 2.50 (0.17), residues: 870 sheet: -0.43 (0.26), residues: 350 loop : -2.31 (0.19), residues: 670 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 297 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 22 residues processed: 316 average time/residue: 0.3070 time to fit residues: 141.5935 Evaluate side-chains 317 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 295 time to evaluate : 1.886 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1634 time to fit residues: 9.4689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 0.0070 chunk 15 optimal weight: 0.0270 chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN G 166 GLN K 187 GLN L 187 GLN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 18152 Z= 0.161 Angle : 0.523 9.097 24901 Z= 0.296 Chirality : 0.039 0.154 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.460 89.446 3054 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.62 % 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: 0.59 (0.19), residues: 1890 helix: 2.58 (0.17), residues: 870 sheet: -0.40 (0.26), residues: 350 loop : -2.28 (0.19), residues: 670 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 307 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 320 average time/residue: 0.3208 time to fit residues: 151.1031 Evaluate side-chains 315 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 298 time to evaluate : 1.975 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2092 time to fit residues: 8.4986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN G 166 GLN I 61 ASN K 187 GLN L 187 GLN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 18152 Z= 0.163 Angle : 0.525 10.623 24901 Z= 0.295 Chirality : 0.039 0.217 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.354 89.826 3054 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.20 % 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: 0.61 (0.19), residues: 1890 helix: 2.62 (0.17), residues: 870 sheet: -0.38 (0.26), residues: 350 loop : -2.30 (0.19), residues: 670 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 309 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 324 average time/residue: 0.3247 time to fit residues: 154.4427 Evaluate side-chains 306 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 301 time to evaluate : 1.922 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1547 time to fit residues: 4.0635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN L 187 GLN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 18152 Z= 0.159 Angle : 0.533 11.348 24901 Z= 0.297 Chirality : 0.039 0.256 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.289 89.977 3054 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.44 % 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: 0.63 (0.19), residues: 1890 helix: 2.63 (0.17), residues: 870 sheet: -0.38 (0.26), residues: 350 loop : -2.29 (0.19), residues: 670 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 302 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 314 average time/residue: 0.3242 time to fit residues: 148.6189 Evaluate side-chains 311 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 300 time to evaluate : 2.007 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2087 time to fit residues: 6.5947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN I 61 ASN L 187 GLN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 18152 Z= 0.188 Angle : 0.555 12.209 24901 Z= 0.308 Chirality : 0.040 0.269 2722 Planarity : 0.003 0.025 2758 Dihedral : 19.302 89.581 3054 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.66 % 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: 0.63 (0.19), residues: 1890 helix: 2.72 (0.17), residues: 860 sheet: -0.39 (0.26), residues: 350 loop : -2.32 (0.18), residues: 680 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 298 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 303 average time/residue: 0.3205 time to fit residues: 142.5580 Evaluate side-chains 301 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 297 time to evaluate : 1.903 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1547 time to fit residues: 3.8347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 121 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN L 187 GLN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 18152 Z= 0.238 Angle : 0.592 13.043 24901 Z= 0.327 Chirality : 0.041 0.264 2722 Planarity : 0.003 0.028 2758 Dihedral : 19.479 89.670 3054 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.48 % 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: 0.55 (0.19), residues: 1890 helix: 2.63 (0.17), residues: 860 sheet: -0.42 (0.26), residues: 350 loop : -2.35 (0.18), residues: 680 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 293 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 295 average time/residue: 0.3366 time to fit residues: 144.2182 Evaluate side-chains 297 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 290 time to evaluate : 1.952 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1811 time to fit residues: 4.9640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 chunk 161 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN H 152 ASN I 61 ASN L 187 GLN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.149399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107081 restraints weight = 22148.258| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.20 r_work: 0.2823 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 18152 Z= 0.184 Angle : 0.554 12.940 24901 Z= 0.308 Chirality : 0.040 0.261 2722 Planarity : 0.003 0.025 2758 Dihedral : 19.418 89.374 3054 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.48 % 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: 0.60 (0.19), residues: 1890 helix: 2.68 (0.17), residues: 860 sheet: -0.42 (0.26), residues: 350 loop : -2.33 (0.18), residues: 680 =============================================================================== Job complete usr+sys time: 3598.59 seconds wall clock time: 66 minutes 7.99 seconds (3967.99 seconds total)