Starting phenix.real_space_refine on Sat Feb 17 05:08:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/02_2024/7ub2_26434.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/02_2024/7ub2_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_26434/02_2024/7ub2_26434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/02_2024/7ub2_26434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/02_2024/7ub2_26434.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/02_2024/7ub2_26434.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.066 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-dev-5238/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: 9.61, per 1000 atoms: 0.55 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: 7.28 Conformation dependent library (CDL) restraints added in 2.7 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: 6.07 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: 5.40 Time building geometry restraints manager: 7.74 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: 8314 17.99 - 35.97: 1745 35.97 - 53.96: 452 53.96 - 71.95: 192 71.95 - 89.94: 27 Dihedral angle restraints: 10730 sinusoidal: 5140 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 10727 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: 3.500 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: 0.000 Extract box with map and model: 5.340 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 50.420 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.730 ------------------------------------------------------------------------------- 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 : 21.081 89.936 7150 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 % Allowed : 29.40 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP J 96 HIS 0.002 0.001 HIS L 185 PHE 0.013 0.001 PHE E 165 TYR 0.019 0.001 TYR E 60 ARG 0.001 0.000 ARG M 132 *********************** 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 : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7631 (tmtt) REVERT: E 203 MET cc_start: 0.4755 (mmm) cc_final: 0.4410 (mmt) REVERT: E 215 LYS cc_start: 0.5444 (mttm) cc_final: 0.5053 (mmtp) REVERT: F 79 MET cc_start: 0.8080 (ttt) cc_final: 0.7876 (tpt) REVERT: F 124 LYS cc_start: 0.7804 (tttm) cc_final: 0.7085 (ttpp) REVERT: F 187 GLN cc_start: 0.6991 (tp40) cc_final: 0.6522 (mm-40) REVERT: G 47 LYS cc_start: 0.8293 (tppp) cc_final: 0.7972 (tptt) REVERT: G 124 LYS cc_start: 0.8060 (tttm) cc_final: 0.7850 (tptt) REVERT: G 166 GLN cc_start: 0.8751 (tt0) cc_final: 0.8529 (tt0) REVERT: G 188 LYS cc_start: 0.8487 (tttt) cc_final: 0.8132 (ttpt) REVERT: H 124 LYS cc_start: 0.8160 (tttm) cc_final: 0.7951 (tttm) REVERT: H 137 LEU cc_start: 0.8124 (mt) cc_final: 0.7917 (mt) REVERT: H 197 LYS cc_start: 0.8567 (ttmm) cc_final: 0.7973 (tttm) REVERT: I 222 ASP cc_start: 0.8287 (m-30) cc_final: 0.7992 (m-30) REVERT: K 40 LYS cc_start: 0.7619 (mtpt) cc_final: 0.7404 (mttt) REVERT: K 68 LYS cc_start: 0.8280 (mmmm) cc_final: 0.7877 (mmmt) REVERT: K 142 LEU cc_start: 0.9381 (tp) cc_final: 0.9154 (tp) REVERT: K 187 GLN cc_start: 0.8565 (tp40) cc_final: 0.8280 (mm-40) REVERT: L 40 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7650 (mttp) REVERT: L 68 LYS cc_start: 0.8328 (mmmm) cc_final: 0.7952 (mmtm) REVERT: L 194 PHE cc_start: 0.9251 (t80) cc_final: 0.9042 (t80) REVERT: L 197 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8426 (mttt) REVERT: M 124 LYS cc_start: 0.7928 (tttm) cc_final: 0.7637 (tttp) REVERT: M 152 ASN cc_start: 0.6673 (t0) cc_final: 0.6416 (p0) REVERT: M 187 GLN cc_start: 0.8140 (tp40) cc_final: 0.7622 (mm-40) REVERT: M 198 LYS cc_start: 0.8424 (mtmt) cc_final: 0.8056 (mtmt) REVERT: N 124 LYS cc_start: 0.7630 (tttm) cc_final: 0.7403 (ttmt) REVERT: N 187 GLN cc_start: 0.7401 (tp40) cc_final: 0.7164 (mm110) outliers start: 10 outliers final: 4 residues processed: 390 average time/residue: 0.3335 time to fit residues: 189.9275 Evaluate side-chains 344 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 340 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain M residue 199 ASP 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: 1.9990 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: 0.7980 chunk 115 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18152 Z= 0.215 Angle : 0.570 7.440 24901 Z= 0.319 Chirality : 0.041 0.190 2722 Planarity : 0.003 0.026 2758 Dihedral : 19.930 89.741 3258 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.23 % Allowed : 26.89 % Favored : 69.88 % 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: 0.76 (0.19), residues: 1890 helix: 2.80 (0.17), residues: 850 sheet: -0.47 (0.25), residues: 350 loop : -2.06 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 177 HIS 0.005 0.002 HIS H 185 PHE 0.024 0.002 PHE K 165 TYR 0.014 0.001 TYR L 200 ARG 0.002 0.000 ARG F 210 *********************** 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 369 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 315 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 MET cc_start: 0.4831 (mmm) cc_final: 0.4111 (mmt) REVERT: E 209 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.6171 (tt) REVERT: F 72 MET cc_start: 0.6190 (mmp) cc_final: 0.5792 (mmp) REVERT: F 79 MET cc_start: 0.8006 (ttt) cc_final: 0.7798 (tpt) REVERT: F 124 LYS cc_start: 0.8103 (tttm) cc_final: 0.7759 (tttp) REVERT: F 187 GLN cc_start: 0.7015 (tp40) cc_final: 0.6554 (mm-40) REVERT: F 188 LYS cc_start: 0.7959 (tptm) cc_final: 0.7499 (ttmt) REVERT: G 166 GLN cc_start: 0.8853 (tt0) cc_final: 0.8602 (tt0) REVERT: G 188 LYS cc_start: 0.8496 (tttt) cc_final: 0.8150 (ttpt) REVERT: H 72 MET cc_start: 0.6683 (tpp) cc_final: 0.6410 (tpp) REVERT: H 124 LYS cc_start: 0.8432 (tttm) cc_final: 0.8227 (tttm) REVERT: H 197 LYS cc_start: 0.8398 (ttmm) cc_final: 0.7840 (tptp) REVERT: I 222 ASP cc_start: 0.8397 (m-30) cc_final: 0.8122 (m-30) REVERT: J 68 LYS cc_start: 0.8518 (mmmm) cc_final: 0.8295 (mmmm) REVERT: J 72 MET cc_start: 0.7739 (tpp) cc_final: 0.7472 (tpp) REVERT: J 124 LYS cc_start: 0.8450 (tttm) cc_final: 0.7913 (ttpp) REVERT: K 40 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7490 (mttt) REVERT: K 68 LYS cc_start: 0.8363 (mmmm) cc_final: 0.7979 (mmmt) REVERT: K 124 LYS cc_start: 0.8146 (tttp) cc_final: 0.7785 (ttpt) REVERT: K 187 GLN cc_start: 0.8557 (tp40) cc_final: 0.8265 (mm-40) REVERT: L 40 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7725 (mttp) REVERT: L 68 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8205 (mmtm) REVERT: L 197 LYS cc_start: 0.8439 (ttmm) cc_final: 0.7983 (mttt) REVERT: M 124 LYS cc_start: 0.8237 (tttm) cc_final: 0.8002 (ttmm) REVERT: M 152 ASN cc_start: 0.6895 (t0) cc_final: 0.6401 (p0) REVERT: M 187 GLN cc_start: 0.8131 (tp40) cc_final: 0.7624 (mm-40) REVERT: M 197 LYS cc_start: 0.7776 (ttmm) cc_final: 0.7356 (mttt) REVERT: M 198 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7730 (mtmt) REVERT: N 124 LYS cc_start: 0.7577 (tttm) cc_final: 0.7286 (ttmt) REVERT: N 187 GLN cc_start: 0.7309 (tp40) cc_final: 0.7087 (mm-40) outliers start: 54 outliers final: 33 residues processed: 350 average time/residue: 0.3093 time to fit residues: 158.9515 Evaluate side-chains 336 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 302 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 I 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 18152 Z= 0.399 Angle : 0.674 9.596 24901 Z= 0.374 Chirality : 0.045 0.225 2722 Planarity : 0.004 0.034 2758 Dihedral : 19.979 89.330 3258 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.45 % Allowed : 24.13 % Favored : 70.42 % 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: 0.31 (0.19), residues: 1890 helix: 2.31 (0.17), residues: 860 sheet: -0.51 (0.25), residues: 350 loop : -2.29 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 177 HIS 0.006 0.003 HIS H 185 PHE 0.030 0.003 PHE K 165 TYR 0.014 0.002 TYR K 200 ARG 0.003 0.000 ARG M 210 *********************** 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 391 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 300 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 MET cc_start: 0.5042 (mmm) cc_final: 0.4740 (mmt) REVERT: E 206 LYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5247 (pttp) REVERT: E 209 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6207 (tt) REVERT: F 79 MET cc_start: 0.8070 (ttt) cc_final: 0.7823 (tpt) REVERT: F 124 LYS cc_start: 0.8291 (tttm) cc_final: 0.7647 (ttpp) REVERT: F 187 GLN cc_start: 0.6867 (tp40) cc_final: 0.6474 (mm-40) REVERT: F 188 LYS cc_start: 0.7807 (tptm) cc_final: 0.7216 (ttmt) REVERT: F 198 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6319 (mtmt) REVERT: G 188 LYS cc_start: 0.8379 (tttt) cc_final: 0.8131 (ttpt) REVERT: G 199 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7915 (p0) REVERT: H 124 LYS cc_start: 0.8700 (tttm) cc_final: 0.8491 (tttm) REVERT: H 180 LYS cc_start: 0.8170 (ttmm) cc_final: 0.7964 (mtpt) REVERT: H 197 LYS cc_start: 0.8480 (ttmm) cc_final: 0.7957 (tptp) REVERT: I 47 LYS cc_start: 0.8649 (tppt) cc_final: 0.8315 (ttmm) REVERT: I 133 GLU cc_start: 0.8627 (tp30) cc_final: 0.8117 (tp30) REVERT: I 222 ASP cc_start: 0.8431 (m-30) cc_final: 0.8160 (m-30) REVERT: J 68 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8505 (mmmm) REVERT: J 72 MET cc_start: 0.7845 (tpp) cc_final: 0.7638 (tpp) REVERT: J 124 LYS cc_start: 0.8615 (tttm) cc_final: 0.8144 (ttpp) REVERT: J 206 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8227 (tttp) REVERT: K 64 ASP cc_start: 0.7832 (p0) cc_final: 0.7591 (p0) REVERT: K 68 LYS cc_start: 0.8463 (mmmm) cc_final: 0.8085 (mmmt) REVERT: K 124 LYS cc_start: 0.8238 (tttp) cc_final: 0.7943 (ttpt) REVERT: K 130 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: K 152 ASN cc_start: 0.8042 (t0) cc_final: 0.7301 (m110) REVERT: L 40 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7868 (mttp) REVERT: L 68 LYS cc_start: 0.8509 (mmmm) cc_final: 0.8265 (mmtm) REVERT: L 180 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7828 (ttpp) REVERT: L 187 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8216 (mm110) REVERT: L 197 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8167 (mttt) REVERT: L 206 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8414 (tttp) REVERT: M 133 GLU cc_start: 0.7053 (tp30) cc_final: 0.6747 (tp30) REVERT: M 136 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7879 (pt) REVERT: M 152 ASN cc_start: 0.7234 (t0) cc_final: 0.6686 (p0) REVERT: M 183 GLU cc_start: 0.8382 (tp30) cc_final: 0.8172 (tp30) REVERT: M 187 GLN cc_start: 0.7977 (tp40) cc_final: 0.7425 (mm-40) REVERT: M 197 LYS cc_start: 0.7776 (ttmm) cc_final: 0.7386 (mttt) REVERT: M 198 LYS cc_start: 0.8334 (mtmt) cc_final: 0.7832 (mtmt) REVERT: N 124 LYS cc_start: 0.7602 (tttm) cc_final: 0.7286 (ttmt) REVERT: N 187 GLN cc_start: 0.7327 (tp40) cc_final: 0.6974 (mm-40) outliers start: 91 outliers final: 57 residues processed: 347 average time/residue: 0.3336 time to fit residues: 166.8722 Evaluate side-chains 362 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 296 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 223 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18152 Z= 0.188 Angle : 0.546 9.581 24901 Z= 0.311 Chirality : 0.041 0.257 2722 Planarity : 0.003 0.029 2758 Dihedral : 19.974 89.336 3258 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.07 % Allowed : 25.75 % Favored : 70.18 % 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: 0.42 (0.19), residues: 1890 helix: 2.46 (0.17), residues: 860 sheet: -0.47 (0.26), residues: 350 loop : -2.33 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 177 HIS 0.004 0.002 HIS G 185 PHE 0.020 0.002 PHE I 165 TYR 0.012 0.001 TYR G 110 ARG 0.002 0.000 ARG M 210 *********************** 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 371 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 303 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 MET cc_start: 0.4965 (mmm) cc_final: 0.4561 (mmt) REVERT: E 206 LYS cc_start: 0.5879 (OUTLIER) cc_final: 0.5048 (pttp) REVERT: F 124 LYS cc_start: 0.8132 (tttm) cc_final: 0.7565 (ttpp) REVERT: F 138 LYS cc_start: 0.6789 (pptt) cc_final: 0.6569 (pptt) REVERT: F 187 GLN cc_start: 0.6883 (tp40) cc_final: 0.6500 (mm-40) REVERT: F 188 LYS cc_start: 0.7821 (tptm) cc_final: 0.7228 (ttmt) REVERT: G 166 GLN cc_start: 0.8871 (tt0) cc_final: 0.8565 (tt0) REVERT: G 188 LYS cc_start: 0.8426 (tttt) cc_final: 0.8173 (ttpt) REVERT: H 72 MET cc_start: 0.6587 (tpp) cc_final: 0.6313 (tpp) REVERT: H 197 LYS cc_start: 0.8423 (ttmm) cc_final: 0.7937 (tptp) REVERT: H 210 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8759 (ttt180) REVERT: I 133 GLU cc_start: 0.8436 (tp30) cc_final: 0.7891 (tp30) REVERT: I 222 ASP cc_start: 0.8423 (m-30) cc_final: 0.8150 (m-30) REVERT: J 68 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8306 (mmmm) REVERT: J 124 LYS cc_start: 0.8482 (tttm) cc_final: 0.7989 (ttpp) REVERT: J 140 ASN cc_start: 0.8057 (p0) cc_final: 0.7687 (p0) REVERT: K 68 LYS cc_start: 0.8452 (mmmm) cc_final: 0.8063 (mmmt) REVERT: K 124 LYS cc_start: 0.8129 (tttp) cc_final: 0.7835 (ttpt) REVERT: K 152 ASN cc_start: 0.7986 (t0) cc_final: 0.7236 (m-40) REVERT: K 206 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8648 (pttp) REVERT: L 40 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7773 (mttp) REVERT: L 68 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8294 (mmtm) REVERT: L 197 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8110 (mttt) REVERT: L 206 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8259 (tttp) REVERT: M 133 GLU cc_start: 0.6894 (tp30) cc_final: 0.6557 (tp30) REVERT: M 136 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7726 (pt) REVERT: M 152 ASN cc_start: 0.7062 (t0) cc_final: 0.6301 (p0) REVERT: M 187 GLN cc_start: 0.8004 (tp40) cc_final: 0.7467 (mm-40) REVERT: M 197 LYS cc_start: 0.7739 (ttmm) cc_final: 0.7387 (mttt) REVERT: M 198 LYS cc_start: 0.8262 (mtmt) cc_final: 0.7751 (mtmt) REVERT: N 124 LYS cc_start: 0.7533 (tttm) cc_final: 0.7209 (ttmt) REVERT: N 187 GLN cc_start: 0.7371 (tp40) cc_final: 0.6960 (mm-40) outliers start: 68 outliers final: 47 residues processed: 346 average time/residue: 0.3227 time to fit residues: 162.8114 Evaluate side-chains 350 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 298 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 159 VAL 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: 1.9990 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 0 optimal weight: 40.0000 chunk 97 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18152 Z= 0.157 Angle : 0.516 8.616 24901 Z= 0.294 Chirality : 0.039 0.214 2722 Planarity : 0.003 0.025 2758 Dihedral : 19.978 89.642 3258 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.19 % Allowed : 25.99 % Favored : 69.82 % 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: 0.51 (0.19), residues: 1890 helix: 2.55 (0.17), residues: 860 sheet: -0.44 (0.26), residues: 350 loop : -2.30 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 96 HIS 0.003 0.002 HIS H 185 PHE 0.019 0.002 PHE I 165 TYR 0.011 0.001 TYR L 110 ARG 0.001 0.000 ARG F 210 *********************** 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 390 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 320 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 124 LYS cc_start: 0.8062 (tttm) cc_final: 0.7411 (ttpp) REVERT: F 187 GLN cc_start: 0.7020 (tp40) cc_final: 0.6550 (mm-40) REVERT: F 188 LYS cc_start: 0.7813 (tptm) cc_final: 0.7206 (ttmt) REVERT: G 166 GLN cc_start: 0.8882 (tt0) cc_final: 0.8626 (tt0) REVERT: G 188 LYS cc_start: 0.8425 (tttt) cc_final: 0.8164 (ttpt) REVERT: H 140 ASN cc_start: 0.7980 (p0) cc_final: 0.7593 (p0) REVERT: H 197 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7928 (tptp) REVERT: I 133 GLU cc_start: 0.8387 (tp30) cc_final: 0.7805 (tp30) REVERT: I 222 ASP cc_start: 0.8446 (m-30) cc_final: 0.8168 (m-30) REVERT: J 68 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8241 (mmmm) REVERT: J 124 LYS cc_start: 0.8428 (tttm) cc_final: 0.7932 (ttpp) REVERT: J 140 ASN cc_start: 0.7909 (p0) cc_final: 0.7508 (p0) REVERT: K 40 LYS cc_start: 0.7694 (mtpt) cc_final: 0.7362 (mttp) REVERT: K 64 ASP cc_start: 0.7910 (p0) cc_final: 0.7610 (p0) REVERT: K 68 LYS cc_start: 0.8415 (mmmm) cc_final: 0.8015 (mmmt) REVERT: K 72 MET cc_start: 0.8123 (mmm) cc_final: 0.7507 (tpp) REVERT: K 124 LYS cc_start: 0.8069 (tttp) cc_final: 0.7763 (ttpt) REVERT: K 152 ASN cc_start: 0.7932 (t0) cc_final: 0.7180 (m-40) REVERT: K 197 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8340 (tppt) REVERT: L 40 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7780 (mttp) REVERT: L 68 LYS cc_start: 0.8478 (mmmm) cc_final: 0.8263 (mmtm) REVERT: L 197 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8093 (mttt) REVERT: M 43 LYS cc_start: 0.7467 (ttmm) cc_final: 0.7246 (mtpp) REVERT: M 133 GLU cc_start: 0.6862 (tp30) cc_final: 0.6539 (tp30) REVERT: M 152 ASN cc_start: 0.7051 (t0) cc_final: 0.6304 (p0) REVERT: M 187 GLN cc_start: 0.8037 (tp40) cc_final: 0.7480 (mm-40) REVERT: M 197 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7376 (mttt) REVERT: M 198 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7662 (mtmt) REVERT: N 72 MET cc_start: 0.4475 (ttm) cc_final: 0.4213 (tpp) REVERT: N 124 LYS cc_start: 0.7523 (tttm) cc_final: 0.7207 (ttmt) REVERT: N 159 VAL cc_start: 0.7328 (OUTLIER) cc_final: 0.6805 (m) REVERT: N 187 GLN cc_start: 0.7397 (tp40) cc_final: 0.6999 (mm-40) outliers start: 70 outliers final: 49 residues processed: 354 average time/residue: 0.3071 time to fit residues: 159.8613 Evaluate side-chains 367 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 316 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.9980 chunk 172 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 88 optimal weight: 0.0060 chunk 15 optimal weight: 0.0020 chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN G 187 GLN I 61 ASN L 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18152 Z= 0.131 Angle : 0.485 7.891 24901 Z= 0.277 Chirality : 0.038 0.209 2722 Planarity : 0.003 0.025 2758 Dihedral : 19.902 89.907 3258 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.07 % Allowed : 25.93 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1890 helix: 2.66 (0.17), residues: 860 sheet: -0.38 (0.27), residues: 350 loop : -2.25 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 96 HIS 0.002 0.001 HIS H 185 PHE 0.016 0.001 PHE I 165 TYR 0.011 0.001 TYR M 110 ARG 0.001 0.000 ARG G 132 *********************** 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 387 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 319 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 MET cc_start: 0.6612 (mtm) cc_final: 0.6374 (tpp) REVERT: E 203 MET cc_start: 0.4778 (mmt) cc_final: 0.4487 (mmt) REVERT: E 206 LYS cc_start: 0.5979 (OUTLIER) cc_final: 0.5267 (ptmm) REVERT: F 124 LYS cc_start: 0.7993 (tttm) cc_final: 0.7339 (ttpt) REVERT: F 187 GLN cc_start: 0.7085 (tp40) cc_final: 0.6617 (mm-40) REVERT: F 188 LYS cc_start: 0.7838 (tptm) cc_final: 0.7220 (ttmt) REVERT: F 198 LYS cc_start: 0.6641 (OUTLIER) cc_final: 0.6141 (mtmt) REVERT: G 68 LYS cc_start: 0.8306 (mmmt) cc_final: 0.7941 (mmtm) REVERT: G 166 GLN cc_start: 0.8848 (tt0) cc_final: 0.8643 (tt0) REVERT: G 188 LYS cc_start: 0.8452 (tttt) cc_final: 0.8156 (ttpt) REVERT: H 72 MET cc_start: 0.6560 (tpp) cc_final: 0.6305 (tpp) REVERT: H 197 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7918 (tptp) REVERT: I 133 GLU cc_start: 0.8321 (tp30) cc_final: 0.7732 (tp30) REVERT: I 222 ASP cc_start: 0.8446 (m-30) cc_final: 0.8166 (m-30) REVERT: J 68 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8200 (mmmm) REVERT: J 124 LYS cc_start: 0.8330 (tttm) cc_final: 0.7833 (ttpp) REVERT: K 40 LYS cc_start: 0.7697 (mtpt) cc_final: 0.7362 (mttp) REVERT: K 64 ASP cc_start: 0.7996 (p0) cc_final: 0.7678 (p0) REVERT: K 68 LYS cc_start: 0.8344 (mmmm) cc_final: 0.7961 (mmmt) REVERT: K 72 MET cc_start: 0.8175 (mmm) cc_final: 0.7545 (tpp) REVERT: K 79 MET cc_start: 0.8996 (ttt) cc_final: 0.8677 (ttm) REVERT: K 124 LYS cc_start: 0.7922 (tttp) cc_final: 0.7606 (ttpt) REVERT: K 197 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8333 (tppt) REVERT: L 40 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7755 (mttp) REVERT: L 68 LYS cc_start: 0.8427 (mmmm) cc_final: 0.8199 (mmtm) REVERT: L 197 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8087 (mttt) REVERT: M 152 ASN cc_start: 0.6946 (t0) cc_final: 0.6263 (p0) REVERT: M 187 GLN cc_start: 0.8106 (tp40) cc_final: 0.7550 (mm-40) REVERT: M 197 LYS cc_start: 0.7804 (ttmm) cc_final: 0.7418 (mttt) REVERT: M 198 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7679 (mtmt) REVERT: N 72 MET cc_start: 0.4466 (ttm) cc_final: 0.4190 (tpp) REVERT: N 124 LYS cc_start: 0.7418 (tttm) cc_final: 0.7099 (ttmt) REVERT: N 159 VAL cc_start: 0.7416 (OUTLIER) cc_final: 0.6883 (m) REVERT: N 187 GLN cc_start: 0.7417 (tp40) cc_final: 0.7065 (mm-40) outliers start: 68 outliers final: 47 residues processed: 359 average time/residue: 0.3013 time to fit residues: 159.4058 Evaluate side-chains 363 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 312 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 190 optimal weight: 8.9990 chunk 119 optimal weight: 0.0050 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN I 169 ASN L 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18152 Z= 0.129 Angle : 0.481 8.676 24901 Z= 0.273 Chirality : 0.038 0.234 2722 Planarity : 0.003 0.023 2758 Dihedral : 19.785 89.999 3258 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.31 % Allowed : 25.27 % Favored : 70.42 % 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: 0.68 (0.19), residues: 1890 helix: 2.66 (0.17), residues: 870 sheet: -0.37 (0.26), residues: 350 loop : -2.23 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 96 HIS 0.002 0.001 HIS K 185 PHE 0.017 0.001 PHE I 165 TYR 0.011 0.001 TYR L 110 ARG 0.001 0.000 ARG F 210 *********************** 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 392 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 320 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 206 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5330 (ttpp) REVERT: F 124 LYS cc_start: 0.7942 (tttm) cc_final: 0.7222 (ttpp) REVERT: F 187 GLN cc_start: 0.7104 (tp40) cc_final: 0.6628 (mm-40) REVERT: F 188 LYS cc_start: 0.7864 (tptm) cc_final: 0.7232 (ttmt) REVERT: F 198 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6067 (mtmt) REVERT: G 166 GLN cc_start: 0.8831 (tt0) cc_final: 0.8611 (tt0) REVERT: G 188 LYS cc_start: 0.8464 (tttt) cc_final: 0.8176 (ttpt) REVERT: H 72 MET cc_start: 0.6647 (tpp) cc_final: 0.6376 (tpp) REVERT: H 197 LYS cc_start: 0.8353 (ttmm) cc_final: 0.7908 (tptp) REVERT: I 133 GLU cc_start: 0.8323 (tp30) cc_final: 0.7697 (tp30) REVERT: I 222 ASP cc_start: 0.8441 (m-30) cc_final: 0.8157 (m-30) REVERT: J 68 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8180 (mmmm) REVERT: J 124 LYS cc_start: 0.8307 (tttm) cc_final: 0.7770 (ttpp) REVERT: K 40 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7367 (mttp) REVERT: K 64 ASP cc_start: 0.8026 (p0) cc_final: 0.7753 (p0) REVERT: K 68 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7942 (mmmt) REVERT: K 72 MET cc_start: 0.8223 (mmm) cc_final: 0.7924 (tpp) REVERT: K 79 MET cc_start: 0.9024 (ttt) cc_final: 0.8648 (ttm) REVERT: K 124 LYS cc_start: 0.7879 (tttp) cc_final: 0.7550 (ttpt) REVERT: K 197 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8334 (tppt) REVERT: L 40 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7741 (mttp) REVERT: L 68 LYS cc_start: 0.8409 (mmmm) cc_final: 0.8181 (mmtm) REVERT: L 197 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8077 (mttt) REVERT: M 152 ASN cc_start: 0.6963 (t0) cc_final: 0.6253 (p0) REVERT: M 187 GLN cc_start: 0.8098 (tp40) cc_final: 0.7558 (mm-40) REVERT: M 197 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7432 (mttt) REVERT: M 198 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7639 (mtmt) REVERT: M 210 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8301 (ttm170) REVERT: N 72 MET cc_start: 0.4476 (ttm) cc_final: 0.4198 (tpp) REVERT: N 124 LYS cc_start: 0.7385 (tttm) cc_final: 0.7075 (ttmt) REVERT: N 159 VAL cc_start: 0.7396 (OUTLIER) cc_final: 0.6854 (m) REVERT: N 187 GLN cc_start: 0.7422 (tp40) cc_final: 0.7068 (mm-40) outliers start: 72 outliers final: 48 residues processed: 360 average time/residue: 0.3005 time to fit residues: 158.4104 Evaluate side-chains 369 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 316 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain M residue 210 ARG Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 113 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18152 Z= 0.216 Angle : 0.543 10.659 24901 Z= 0.306 Chirality : 0.040 0.244 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.808 89.977 3258 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.13 % Allowed : 25.09 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1890 helix: 2.70 (0.17), residues: 860 sheet: -0.41 (0.26), residues: 350 loop : -2.29 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 177 HIS 0.004 0.002 HIS H 185 PHE 0.022 0.002 PHE K 165 TYR 0.011 0.001 TYR G 110 ARG 0.003 0.000 ARG L 210 *********************** 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 373 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 304 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 206 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.5198 (pptt) REVERT: E 209 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6169 (tt) REVERT: F 124 LYS cc_start: 0.8162 (tttm) cc_final: 0.7554 (ttpp) REVERT: F 132 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.6015 (mtp180) REVERT: F 135 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7954 (mt-10) REVERT: F 183 GLU cc_start: 0.7292 (tm-30) cc_final: 0.7000 (tm-30) REVERT: F 187 GLN cc_start: 0.7067 (tp40) cc_final: 0.6523 (mm-40) REVERT: F 188 LYS cc_start: 0.7838 (tptm) cc_final: 0.7243 (ttmt) REVERT: F 198 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6465 (mtmt) REVERT: G 64 ASP cc_start: 0.8025 (p0) cc_final: 0.7775 (p0) REVERT: G 188 LYS cc_start: 0.8470 (tttt) cc_final: 0.8208 (ttpt) REVERT: H 68 LYS cc_start: 0.8465 (mptt) cc_final: 0.8243 (mptt) REVERT: H 72 MET cc_start: 0.6692 (tpp) cc_final: 0.6419 (tpp) REVERT: H 140 ASN cc_start: 0.8132 (p0) cc_final: 0.7681 (p0) REVERT: H 197 LYS cc_start: 0.8404 (ttmm) cc_final: 0.7909 (tptp) REVERT: I 133 GLU cc_start: 0.8463 (tp30) cc_final: 0.7872 (tp30) REVERT: I 222 ASP cc_start: 0.8465 (m-30) cc_final: 0.8173 (m-30) REVERT: J 68 LYS cc_start: 0.8638 (mmmm) cc_final: 0.8249 (mmmm) REVERT: J 124 LYS cc_start: 0.8493 (tttm) cc_final: 0.7999 (ttpp) REVERT: J 140 ASN cc_start: 0.7941 (p0) cc_final: 0.7533 (p0) REVERT: K 40 LYS cc_start: 0.7715 (mtpt) cc_final: 0.7400 (mttp) REVERT: K 64 ASP cc_start: 0.8036 (p0) cc_final: 0.7790 (p0) REVERT: K 68 LYS cc_start: 0.8428 (mmmm) cc_final: 0.8030 (mmmt) REVERT: K 72 MET cc_start: 0.8160 (mmm) cc_final: 0.7902 (tpp) REVERT: K 124 LYS cc_start: 0.8073 (tttp) cc_final: 0.7761 (ttpt) REVERT: K 152 ASN cc_start: 0.7934 (t0) cc_final: 0.7180 (m-40) REVERT: K 197 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8361 (tppt) REVERT: L 68 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8261 (mmtm) REVERT: L 197 LYS cc_start: 0.8635 (ttmm) cc_final: 0.8182 (mttt) REVERT: M 152 ASN cc_start: 0.7028 (t0) cc_final: 0.6248 (p0) REVERT: M 187 GLN cc_start: 0.8043 (tp40) cc_final: 0.7479 (mm-40) REVERT: M 198 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7781 (mtmt) REVERT: M 210 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8387 (ttm170) REVERT: N 72 MET cc_start: 0.4523 (ttm) cc_final: 0.4242 (tpp) REVERT: N 124 LYS cc_start: 0.7534 (tttm) cc_final: 0.7220 (ttmt) REVERT: N 159 VAL cc_start: 0.7377 (OUTLIER) cc_final: 0.6796 (m) REVERT: N 187 GLN cc_start: 0.7411 (tp40) cc_final: 0.6893 (mm-40) outliers start: 69 outliers final: 54 residues processed: 338 average time/residue: 0.3357 time to fit residues: 168.1814 Evaluate side-chains 362 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 301 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain M residue 210 ARG Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 157 LYS Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18152 Z= 0.171 Angle : 0.524 10.703 24901 Z= 0.296 Chirality : 0.040 0.268 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.801 89.965 3258 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.65 % Allowed : 25.63 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1890 helix: 2.68 (0.17), residues: 860 sheet: -0.40 (0.26), residues: 350 loop : -2.28 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 177 HIS 0.003 0.002 HIS H 185 PHE 0.020 0.002 PHE I 165 TYR 0.011 0.001 TYR L 110 ARG 0.002 0.000 ARG F 210 *********************** 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 367 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 306 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 MET cc_start: 0.7030 (tpp) cc_final: 0.5992 (mtm) REVERT: E 206 LYS cc_start: 0.5895 (OUTLIER) cc_final: 0.5254 (pptt) REVERT: F 124 LYS cc_start: 0.8120 (tttm) cc_final: 0.7770 (tttp) REVERT: F 183 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7056 (tm-30) REVERT: F 187 GLN cc_start: 0.7060 (tp40) cc_final: 0.6509 (mm-40) REVERT: F 188 LYS cc_start: 0.7848 (tptm) cc_final: 0.7235 (ttmt) REVERT: F 198 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6476 (mtmt) REVERT: G 64 ASP cc_start: 0.8026 (p0) cc_final: 0.7762 (p0) REVERT: G 188 LYS cc_start: 0.8427 (tttt) cc_final: 0.8164 (ttpt) REVERT: H 72 MET cc_start: 0.6685 (tpp) cc_final: 0.6418 (tpp) REVERT: H 140 ASN cc_start: 0.8063 (p0) cc_final: 0.7630 (p0) REVERT: H 197 LYS cc_start: 0.8396 (ttmm) cc_final: 0.7909 (tptp) REVERT: I 133 GLU cc_start: 0.8433 (tp30) cc_final: 0.7834 (tp30) REVERT: I 222 ASP cc_start: 0.8472 (m-30) cc_final: 0.8188 (m-30) REVERT: J 68 LYS cc_start: 0.8641 (mmmm) cc_final: 0.8247 (mmmm) REVERT: J 124 LYS cc_start: 0.8456 (tttm) cc_final: 0.7972 (ttpp) REVERT: J 140 ASN cc_start: 0.7883 (p0) cc_final: 0.7475 (p0) REVERT: K 40 LYS cc_start: 0.7652 (mtpt) cc_final: 0.7315 (mttp) REVERT: K 64 ASP cc_start: 0.8057 (p0) cc_final: 0.7844 (p0) REVERT: K 68 LYS cc_start: 0.8390 (mmmm) cc_final: 0.7974 (mmmt) REVERT: K 72 MET cc_start: 0.8195 (mmm) cc_final: 0.7928 (tpp) REVERT: K 124 LYS cc_start: 0.8009 (tttp) cc_final: 0.7709 (ttpt) REVERT: K 152 ASN cc_start: 0.7931 (t0) cc_final: 0.7177 (m-40) REVERT: K 197 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8348 (tppt) REVERT: L 40 LYS cc_start: 0.8222 (mttp) cc_final: 0.7851 (mttm) REVERT: L 68 LYS cc_start: 0.8444 (mmmm) cc_final: 0.8230 (mmtm) REVERT: L 197 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8107 (mttt) REVERT: M 152 ASN cc_start: 0.6970 (t0) cc_final: 0.6230 (p0) REVERT: M 187 GLN cc_start: 0.8073 (tp40) cc_final: 0.7512 (mm-40) REVERT: M 198 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7787 (mtmt) REVERT: M 210 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8374 (ttm170) REVERT: N 72 MET cc_start: 0.4437 (ttm) cc_final: 0.4179 (tpp) REVERT: N 124 LYS cc_start: 0.7480 (tttm) cc_final: 0.7171 (ttmt) REVERT: N 187 GLN cc_start: 0.7425 (tp40) cc_final: 0.6909 (mm-40) outliers start: 61 outliers final: 53 residues processed: 336 average time/residue: 0.3105 time to fit residues: 153.5792 Evaluate side-chains 360 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 304 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain M residue 210 ARG Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 157 LYS Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 130 optimal weight: 0.0980 chunk 197 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18152 Z= 0.144 Angle : 0.506 10.283 24901 Z= 0.285 Chirality : 0.039 0.268 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.744 89.862 3258 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.59 % Allowed : 26.05 % Favored : 70.36 % 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: 0.66 (0.19), residues: 1890 helix: 2.64 (0.17), residues: 870 sheet: -0.38 (0.26), residues: 350 loop : -2.22 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 96 HIS 0.003 0.001 HIS K 185 PHE 0.018 0.001 PHE I 165 TYR 0.011 0.001 TYR L 110 ARG 0.001 0.000 ARG L 210 ********************** 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 368 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 308 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 MET cc_start: 0.6995 (tpp) cc_final: 0.5903 (mtm) REVERT: E 206 LYS cc_start: 0.5974 (OUTLIER) cc_final: 0.5122 (pttp) REVERT: F 124 LYS cc_start: 0.7995 (tttm) cc_final: 0.7648 (tttp) REVERT: F 132 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.5949 (mtp85) REVERT: F 183 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7081 (tm-30) REVERT: F 187 GLN cc_start: 0.7038 (tp40) cc_final: 0.6563 (mm-40) REVERT: F 188 LYS cc_start: 0.7852 (tptm) cc_final: 0.7228 (ttmt) REVERT: F 198 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6510 (mtmt) REVERT: G 64 ASP cc_start: 0.7983 (p0) cc_final: 0.7710 (p0) REVERT: G 188 LYS cc_start: 0.8460 (tttt) cc_final: 0.8189 (ttpt) REVERT: H 72 MET cc_start: 0.6659 (tpp) cc_final: 0.6371 (tpp) REVERT: H 197 LYS cc_start: 0.8398 (ttmm) cc_final: 0.7924 (tptp) REVERT: I 133 GLU cc_start: 0.8413 (tp30) cc_final: 0.7831 (tp30) REVERT: I 222 ASP cc_start: 0.8466 (m-30) cc_final: 0.8181 (m-30) REVERT: J 68 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8223 (mmmm) REVERT: J 124 LYS cc_start: 0.8373 (tttm) cc_final: 0.7831 (ttpp) REVERT: K 40 LYS cc_start: 0.7615 (mtpt) cc_final: 0.7282 (mttp) REVERT: K 68 LYS cc_start: 0.8353 (mmmm) cc_final: 0.7968 (mmmt) REVERT: K 72 MET cc_start: 0.8187 (mmm) cc_final: 0.7918 (tpp) REVERT: K 124 LYS cc_start: 0.7963 (tttp) cc_final: 0.7648 (ttpt) REVERT: K 197 LYS cc_start: 0.8594 (ttmm) cc_final: 0.8349 (tppt) REVERT: L 40 LYS cc_start: 0.8082 (mttp) cc_final: 0.7765 (mttm) REVERT: L 68 LYS cc_start: 0.8436 (mmmm) cc_final: 0.8210 (mmtm) REVERT: L 197 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8106 (mttt) REVERT: M 152 ASN cc_start: 0.6951 (t0) cc_final: 0.6205 (p0) REVERT: M 187 GLN cc_start: 0.8119 (tp40) cc_final: 0.7563 (mm-40) REVERT: M 198 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7689 (mtmt) REVERT: M 210 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8330 (ttm170) REVERT: N 124 LYS cc_start: 0.7390 (tttm) cc_final: 0.7083 (ttmt) REVERT: N 187 GLN cc_start: 0.7468 (tp40) cc_final: 0.6958 (mm-40) outliers start: 60 outliers final: 51 residues processed: 339 average time/residue: 0.3099 time to fit residues: 154.7714 Evaluate side-chains 360 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 305 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 37 MET Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain M residue 210 ARG Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 157 LYS Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.6980 chunk 48 optimal weight: 0.0170 chunk 144 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 157 optimal weight: 0.0870 chunk 65 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN K 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.154727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.113394 restraints weight = 22146.255| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.26 r_work: 0.2864 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18152 Z= 0.134 Angle : 0.499 11.311 24901 Z= 0.278 Chirality : 0.039 0.274 2722 Planarity : 0.003 0.023 2758 Dihedral : 19.652 89.970 3258 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.29 % Allowed : 26.35 % Favored : 70.36 % 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: 0.73 (0.19), residues: 1890 helix: 2.69 (0.17), residues: 870 sheet: -0.35 (0.26), residues: 350 loop : -2.18 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 96 HIS 0.002 0.001 HIS K 185 PHE 0.016 0.001 PHE I 165 TYR 0.011 0.001 TYR M 110 ARG 0.001 0.000 ARG F 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3852.47 seconds wall clock time: 70 minutes 44.84 seconds (4244.84 seconds total)