Starting phenix.real_space_refine on Wed Feb 4 16:31:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tgo_55906/02_2026/9tgo_55906.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tgo_55906/02_2026/9tgo_55906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tgo_55906/02_2026/9tgo_55906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tgo_55906/02_2026/9tgo_55906.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tgo_55906/02_2026/9tgo_55906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tgo_55906/02_2026/9tgo_55906.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.008 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 15 5.21 5 S 66 5.16 5 C 7169 2.51 5 N 1962 2.21 5 O 2416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11676 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "B" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "O" Number of atoms: 247 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Conformer: "B" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} bond proxies already assigned to first conformer: 273 Chain: "P" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "F" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "I" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "J" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "K" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "M" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "S" Number of atoms: 246 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 12, 245 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 12, 245 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 271 Chain: "T" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "L" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "N" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "O" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.96, per 1000 atoms: 0.25 Number of scatterers: 11676 At special positions: 0 Unit cell: (116.28, 110.2, 149.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 48 15.00 Mg 15 11.99 O 2416 8.00 N 1962 7.00 C 7169 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 98 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 98 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 98 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 98 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 98 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.88 Conformation dependent library (CDL) restraints added in 486.3 milliseconds 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2496 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 35 sheets defined 7.0% alpha, 45.3% beta 23 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.663A pdb=" N THR A 31 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.044A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.716A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.921A pdb=" N THR C 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.745A pdb=" N ILE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.544A pdb=" N THR D 31 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.827A pdb=" N THR D 93 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.692A pdb=" N THR I 31 " --> pdb=" O ASN I 28 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 89 through 93 removed outlier: 3.703A pdb=" N ASP I 92 " --> pdb=" O LYS I 89 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR I 93 " --> pdb=" O ALA I 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 89 through 93' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.955A pdb=" N ILE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.755A pdb=" N THR K 31 " --> pdb=" O ASN K 28 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 53 through 57 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.902A pdb=" N ILE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.662A pdb=" N THR L 31 " --> pdb=" O ASN L 28 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 32' Processing helix chain 'L' and resid 53 through 57 Processing helix chain 'L' and resid 89 through 93 removed outlier: 4.272A pdb=" N THR L 93 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.392A pdb=" N GLY A 10 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N MET A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.392A pdb=" N GLY A 10 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR A 111 " --> pdb=" O ARG A 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.669A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.082A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 24 removed outlier: 3.729A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.953A pdb=" N MET C 34 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.601A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.157A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.157A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN E 90 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.340A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.340A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR D 111 " --> pdb=" O ARG D 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.593A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.261A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 48 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.261A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.735A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET I 85 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.735A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.063A pdb=" N MET I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ARG I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AC5, first strand: chain 'J' and resid 44 through 49 removed outlier: 5.562A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.688A pdb=" N LEU K 83 " --> pdb=" O LEU K 20 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.289A pdb=" N GLY K 10 " --> pdb=" O THR K 119 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.289A pdb=" N GLY K 10 " --> pdb=" O THR K 119 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR K 111 " --> pdb=" O ARG K 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.103A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AD2, first strand: chain 'M' and resid 89 through 90 removed outlier: 3.747A pdb=" N GLN M 90 " --> pdb=" O THR M 97 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'L' and resid 3 through 7 removed outlier: 3.503A pdb=" N SER L 73 " --> pdb=" O TYR L 82 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.892A pdb=" N MET L 34 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.942A pdb=" N TYR L 111 " --> pdb=" O ARG L 100 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.604A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.050A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.050A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN N 90 " --> pdb=" O THR N 97 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3544 1.34 - 1.46: 3166 1.46 - 1.58: 5062 1.58 - 1.70: 94 1.70 - 1.82: 108 Bond restraints: 11974 Sorted by residual: bond pdb=" N1 DC S 11 " pdb=" C2 DC S 11 " ideal model delta sigma weight residual 1.399 1.429 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C2 DC S 11 " pdb=" N3 DC S 11 " ideal model delta sigma weight residual 1.356 1.385 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" CB GLN I 13 " pdb=" CG GLN I 13 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" C3' DG S 8 " pdb=" O3' DG S 8 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" C ALA I 40 " pdb=" N PRO I 41 " ideal model delta sigma weight residual 1.332 1.346 -0.014 1.12e-02 7.97e+03 1.56e+00 ... (remaining 11969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 16241 2.48 - 4.97: 133 4.97 - 7.45: 18 7.45 - 9.94: 3 9.94 - 12.42: 1 Bond angle restraints: 16396 Sorted by residual: angle pdb=" CA GLN I 13 " pdb=" CB GLN I 13 " pdb=" CG GLN I 13 " ideal model delta sigma weight residual 114.10 122.66 -8.56 2.00e+00 2.50e-01 1.83e+01 angle pdb=" CB MET I 34 " pdb=" CG MET I 34 " pdb=" SD MET I 34 " ideal model delta sigma weight residual 112.70 125.12 -12.42 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB GLN I 13 " pdb=" CG GLN I 13 " pdb=" CD GLN I 13 " ideal model delta sigma weight residual 112.60 119.13 -6.53 1.70e+00 3.46e-01 1.48e+01 angle pdb=" N LYS L 67 " pdb=" CA LYS L 67 " pdb=" C LYS L 67 " ideal model delta sigma weight residual 114.04 109.76 4.28 1.24e+00 6.50e-01 1.19e+01 angle pdb=" C TYR B 50 " pdb=" N THR B 51 " pdb=" CA THR B 51 " ideal model delta sigma weight residual 121.54 128.09 -6.55 1.91e+00 2.74e-01 1.18e+01 ... (remaining 16391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.87: 6290 29.87 - 59.75: 574 59.75 - 89.62: 52 89.62 - 119.49: 2 119.49 - 149.37: 2 Dihedral angle restraints: 6920 sinusoidal: 2972 harmonic: 3948 Sorted by residual: dihedral pdb=" CB CYS M 23 " pdb=" SG CYS M 23 " pdb=" SG CYS M 88 " pdb=" CB CYS M 88 " ideal model delta sinusoidal sigma weight residual -86.00 -169.68 83.68 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 140.25 -47.25 1 1.00e+01 1.00e-02 3.08e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 138.65 -45.65 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 6917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1309 0.041 - 0.082: 303 0.082 - 0.123: 143 0.123 - 0.164: 12 0.164 - 0.205: 5 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CB ILE M 8 " pdb=" CA ILE M 8 " pdb=" CG1 ILE M 8 " pdb=" CG2 ILE M 8 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PHE F 94 " pdb=" N PHE F 94 " pdb=" C PHE F 94 " pdb=" CB PHE F 94 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA PHE E 94 " pdb=" N PHE E 94 " pdb=" C PHE E 94 " pdb=" CB PHE E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 1769 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN I 13 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO I 14 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO I 14 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 14 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO I 14 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C PRO I 14 " 0.028 2.00e-02 2.50e+03 pdb=" O PRO I 14 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS I 15 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 79 " -0.025 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO B 80 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.022 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 319 2.70 - 3.25: 9759 3.25 - 3.80: 17497 3.80 - 4.35: 23841 4.35 - 4.90: 40614 Nonbonded interactions: 92030 Sorted by model distance: nonbonded pdb=" N2 DG O 12 " pdb="MG MG O 106 " model vdw 2.148 2.250 nonbonded pdb=" N2 DG S 6 " pdb="MG MG S 105 " model vdw 2.415 2.250 nonbonded pdb=" OE1 GLN I 13 " pdb=" O PRO I 14 " model vdw 2.473 3.040 nonbonded pdb=" O5' DG O 6 " pdb=" O4' DG O 6 " model vdw 2.530 2.432 nonbonded pdb=" N2 DG S 10 " pdb="MG MG S 102 " model vdw 2.547 2.250 ... (remaining 92025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = (chain 'O' and (resid 1 through 5 or resid 7 through 10 or (resid 11 and (name P \ or name OP1 or name OP2 or name O5' or name C5' or name C4' or name O4' or name \ C3' or name O3' or name C2' or name C1' or name N1 or name C2 or name O2 or nam \ e N3 or name C4 or name N4 or name C6 )) or resid 12 through 105)) selection = (chain 'S' and (resid 1 through 5 or resid 7 through 105)) } ncs_group { reference = chain 'P' selection = chain 'T' } 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=0.02 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.090 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 0.042 11986 Z= 0.141 Angle : 0.599 12.421 16420 Z= 0.330 Chirality : 0.043 0.205 1772 Planarity : 0.004 0.058 1920 Dihedral : 20.201 149.367 4388 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.17 % Favored : 97.68 % Rotamer: Outliers : 2.92 % Allowed : 33.68 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.07 (0.21), residues: 654 loop : -0.89 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 18 TYR 0.019 0.001 TYR J 49 PHE 0.020 0.001 PHE F 94 TRP 0.021 0.001 TRP I 47 HIS 0.001 0.000 HIS J 55 Details of bonding type rmsd covalent geometry : bond 0.00296 (11974) covalent geometry : angle 0.59917 (16396) SS BOND : bond 0.00407 ( 12) SS BOND : angle 0.72078 ( 24) hydrogen bonds : bond 0.22208 ( 425) hydrogen bonds : angle 8.75590 ( 1077) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: C 3 GLN cc_start: 0.8817 (mt0) cc_final: 0.8536 (mm-40) REVERT: E 45 LYS cc_start: 0.8444 (mtpm) cc_final: 0.8205 (mttm) REVERT: E 77 ASN cc_start: 0.8059 (p0) cc_final: 0.7815 (p0) REVERT: D 80 MET cc_start: 0.9297 (mmm) cc_final: 0.9017 (tpt) REVERT: K 17 SER cc_start: 0.7838 (m) cc_final: 0.7638 (m) REVERT: K 111 TYR cc_start: 0.7663 (m-80) cc_final: 0.7026 (t80) REVERT: N 11 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5896 (tm) REVERT: N 53 ARG cc_start: 0.6740 (mtt180) cc_final: 0.6491 (mmm-85) outliers start: 34 outliers final: 12 residues processed: 273 average time/residue: 0.5068 time to fit residues: 150.7182 Evaluate side-chains 223 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 44 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN C 28 ASN C 39 GLN E 38 GLN D 3 GLN D 84 GLN D 87 ASN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 39 GLN K 87 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 89 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.153285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.121022 restraints weight = 14187.726| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.00 r_work: 0.3180 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11986 Z= 0.266 Angle : 0.691 8.219 16420 Z= 0.381 Chirality : 0.050 0.285 1772 Planarity : 0.005 0.041 1920 Dihedral : 16.619 157.909 2000 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.59 % Favored : 96.26 % Rotamer: Outliers : 6.87 % Allowed : 28.95 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.25 (0.21), residues: 654 loop : -0.91 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 18 TYR 0.020 0.002 TYR L 97 PHE 0.036 0.003 PHE F 94 TRP 0.014 0.002 TRP I 47 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00615 (11974) covalent geometry : angle 0.68973 (16396) SS BOND : bond 0.00872 ( 12) SS BOND : angle 1.34105 ( 24) hydrogen bonds : bond 0.04418 ( 425) hydrogen bonds : angle 5.55507 ( 1077) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 193 time to evaluate : 0.264 Fit side-chains REVERT: C 15 LYS cc_start: 0.8771 (mttt) cc_final: 0.8098 (mmtt) REVERT: C 43 LYS cc_start: 0.8187 (mptt) cc_final: 0.7917 (mptt) REVERT: E 12 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.7918 (m) REVERT: E 41 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8129 (p0) REVERT: E 77 ASN cc_start: 0.7843 (p0) cc_final: 0.7458 (p0) REVERT: I 66 MET cc_start: 0.5290 (mpp) cc_final: 0.5059 (mtt) REVERT: I 85 MET cc_start: 0.5213 (OUTLIER) cc_final: 0.4913 (pmt) REVERT: I 110 ASP cc_start: 0.5321 (OUTLIER) cc_final: 0.5037 (p0) REVERT: J 33 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6972 (tp) REVERT: K 85 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7437 (mtp) REVERT: K 111 TYR cc_start: 0.7359 (m-80) cc_final: 0.6525 (t80) REVERT: N 11 LEU cc_start: 0.5028 (OUTLIER) cc_final: 0.4540 (tm) REVERT: N 86 TYR cc_start: 0.7068 (m-80) cc_final: 0.6862 (m-80) outliers start: 80 outliers final: 36 residues processed: 248 average time/residue: 0.4057 time to fit residues: 110.8487 Evaluate side-chains 232 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain I residue 110 ASP Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 21 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 82 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN B 31 ASN C 87 ASN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 87 ASN L 79 ASN L 101 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.156535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.124715 restraints weight = 14292.169| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.04 r_work: 0.3235 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11986 Z= 0.128 Angle : 0.554 6.454 16420 Z= 0.305 Chirality : 0.044 0.220 1772 Planarity : 0.004 0.039 1920 Dihedral : 16.414 153.228 1990 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.47 % Favored : 97.38 % Rotamer: Outliers : 5.84 % Allowed : 29.04 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.41 (0.21), residues: 654 loop : -0.76 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 18 TYR 0.012 0.001 TYR L 97 PHE 0.027 0.002 PHE F 94 TRP 0.010 0.001 TRP I 47 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00278 (11974) covalent geometry : angle 0.55343 (16396) SS BOND : bond 0.00502 ( 12) SS BOND : angle 0.87901 ( 24) hydrogen bonds : bond 0.03089 ( 425) hydrogen bonds : angle 4.93501 ( 1077) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 193 time to evaluate : 0.322 Fit side-chains REVERT: A 1 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8028 (ptmm) REVERT: C 15 LYS cc_start: 0.8737 (mttt) cc_final: 0.8062 (mmtt) REVERT: E 12 SER cc_start: 0.8310 (OUTLIER) cc_final: 0.7933 (m) REVERT: E 77 ASN cc_start: 0.7619 (p0) cc_final: 0.7325 (p0) REVERT: E 105 GLU cc_start: 0.8335 (tt0) cc_final: 0.8088 (pt0) REVERT: I 85 MET cc_start: 0.5415 (OUTLIER) cc_final: 0.5121 (pmt) REVERT: J 33 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7164 (tt) REVERT: K 105 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.7233 (t0) REVERT: K 111 TYR cc_start: 0.7391 (m-80) cc_final: 0.6547 (t80) REVERT: M 3 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7985 (mt0) REVERT: N 11 LEU cc_start: 0.4983 (OUTLIER) cc_final: 0.4525 (tm) outliers start: 68 outliers final: 31 residues processed: 239 average time/residue: 0.4413 time to fit residues: 115.4496 Evaluate side-chains 228 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 105 ASN Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 37 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 114 GLN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 39 GLN K 87 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.119495 restraints weight = 14365.481| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.09 r_work: 0.3159 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11986 Z= 0.267 Angle : 0.674 8.389 16420 Z= 0.372 Chirality : 0.050 0.287 1772 Planarity : 0.004 0.038 1920 Dihedral : 16.563 157.222 1988 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.26 % Rotamer: Outliers : 7.13 % Allowed : 27.32 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.40 (0.20), residues: 654 loop : -0.80 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 18 TYR 0.021 0.002 TYR L 97 PHE 0.036 0.002 PHE F 94 TRP 0.011 0.001 TRP I 47 HIS 0.003 0.001 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00624 (11974) covalent geometry : angle 0.67280 (16396) SS BOND : bond 0.00772 ( 12) SS BOND : angle 1.27973 ( 24) hydrogen bonds : bond 0.04082 ( 425) hydrogen bonds : angle 5.06143 ( 1077) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 190 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: B 81 GLU cc_start: 0.7836 (pp20) cc_final: 0.7517 (pp20) REVERT: C 15 LYS cc_start: 0.8737 (mttt) cc_final: 0.8042 (mmtt) REVERT: E 12 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.7842 (m) REVERT: E 41 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8161 (p0) REVERT: E 77 ASN cc_start: 0.7813 (p0) cc_final: 0.7427 (p0) REVERT: D 95 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8682 (ttp) REVERT: I 66 MET cc_start: 0.5249 (mpp) cc_final: 0.4947 (mtt) REVERT: I 85 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.5086 (pmt) REVERT: I 110 ASP cc_start: 0.5638 (OUTLIER) cc_final: 0.5414 (p0) REVERT: J 33 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7184 (tp) REVERT: K 105 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7377 (t0) REVERT: K 111 TYR cc_start: 0.7453 (m-80) cc_final: 0.6508 (t80) REVERT: M 45 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8236 (mttp) outliers start: 83 outliers final: 50 residues processed: 247 average time/residue: 0.4251 time to fit residues: 115.2281 Evaluate side-chains 246 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain I residue 110 ASP Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 105 ASN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 22 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 114 GLN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 87 ASN M 34 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN N 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.151947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.120071 restraints weight = 14436.208| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.02 r_work: 0.3171 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11986 Z= 0.246 Angle : 0.660 8.059 16420 Z= 0.364 Chirality : 0.049 0.286 1772 Planarity : 0.004 0.038 1920 Dihedral : 16.504 156.023 1986 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.01 % Rotamer: Outliers : 6.79 % Allowed : 27.58 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.42 (0.21), residues: 654 loop : -0.83 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 18 TYR 0.020 0.002 TYR L 97 PHE 0.038 0.002 PHE F 94 TRP 0.012 0.001 TRP I 47 HIS 0.003 0.001 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00573 (11974) covalent geometry : angle 0.65912 (16396) SS BOND : bond 0.00768 ( 12) SS BOND : angle 1.18801 ( 24) hydrogen bonds : bond 0.03825 ( 425) hydrogen bonds : angle 4.95077 ( 1077) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 197 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: B 81 GLU cc_start: 0.7924 (pp20) cc_final: 0.7586 (pp20) REVERT: C 15 LYS cc_start: 0.8733 (mttt) cc_final: 0.8008 (mmtt) REVERT: C 67 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8004 (tttp) REVERT: E 12 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7834 (m) REVERT: E 41 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8130 (p0) REVERT: E 77 ASN cc_start: 0.7776 (p0) cc_final: 0.7441 (p0) REVERT: D 95 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8653 (ttp) REVERT: F 53 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7911 (mmt180) REVERT: I 85 MET cc_start: 0.5358 (OUTLIER) cc_final: 0.5101 (pmt) REVERT: I 110 ASP cc_start: 0.5686 (OUTLIER) cc_final: 0.5471 (p0) REVERT: J 33 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7169 (tp) REVERT: K 105 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7363 (t0) REVERT: K 111 TYR cc_start: 0.7432 (m-80) cc_final: 0.6495 (t80) REVERT: M 45 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8224 (mttp) outliers start: 79 outliers final: 52 residues processed: 255 average time/residue: 0.4649 time to fit residues: 130.2819 Evaluate side-chains 252 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain I residue 110 ASP Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 105 ASN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 127 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 114 GLN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 39 GLN K 87 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.153530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121861 restraints weight = 14312.554| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.95 r_work: 0.3191 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11986 Z= 0.173 Angle : 0.596 7.503 16420 Z= 0.328 Chirality : 0.046 0.253 1772 Planarity : 0.004 0.037 1920 Dihedral : 16.339 155.015 1986 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.21 % Favored : 96.71 % Rotamer: Outliers : 6.53 % Allowed : 27.75 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.48 (0.21), residues: 654 loop : -0.71 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 18 TYR 0.015 0.002 TYR J 49 PHE 0.032 0.002 PHE F 94 TRP 0.012 0.001 TRP I 47 HIS 0.001 0.001 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00395 (11974) covalent geometry : angle 0.59538 (16396) SS BOND : bond 0.00628 ( 12) SS BOND : angle 0.92980 ( 24) hydrogen bonds : bond 0.03236 ( 425) hydrogen bonds : angle 4.71093 ( 1077) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 191 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 81 GLU cc_start: 0.7905 (pp20) cc_final: 0.7607 (pp20) REVERT: C 15 LYS cc_start: 0.8746 (mttt) cc_final: 0.8032 (mmtt) REVERT: C 43 LYS cc_start: 0.8201 (mptt) cc_final: 0.7968 (mptt) REVERT: E 12 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7870 (m) REVERT: E 41 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8024 (p0) REVERT: E 77 ASN cc_start: 0.7739 (p0) cc_final: 0.7481 (p0) REVERT: D 95 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8636 (ttp) REVERT: I 85 MET cc_start: 0.5321 (OUTLIER) cc_final: 0.5081 (pmt) REVERT: J 33 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7033 (tt) REVERT: K 105 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7440 (t0) REVERT: K 111 TYR cc_start: 0.7450 (m-80) cc_final: 0.6574 (t80) REVERT: M 3 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8121 (mt0) outliers start: 76 outliers final: 53 residues processed: 248 average time/residue: 0.4539 time to fit residues: 124.0832 Evaluate side-chains 249 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 105 ASN Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 77 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 114 GLN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 87 ASN M 34 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.148894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103544 restraints weight = 14814.812| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.24 r_work: 0.3184 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11986 Z= 0.248 Angle : 0.671 9.142 16420 Z= 0.368 Chirality : 0.049 0.286 1772 Planarity : 0.004 0.039 1920 Dihedral : 16.516 156.884 1986 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 6.79 % Allowed : 28.18 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.46 (0.21), residues: 654 loop : -0.80 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 18 TYR 0.020 0.002 TYR L 97 PHE 0.037 0.002 PHE F 94 TRP 0.016 0.001 TRP I 47 HIS 0.003 0.001 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00578 (11974) covalent geometry : angle 0.66994 (16396) SS BOND : bond 0.00766 ( 12) SS BOND : angle 1.20177 ( 24) hydrogen bonds : bond 0.03848 ( 425) hydrogen bonds : angle 4.88527 ( 1077) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 198 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7137 (mm-40) cc_final: 0.6818 (mp10) REVERT: B 81 GLU cc_start: 0.7979 (pp20) cc_final: 0.7533 (pp20) REVERT: C 15 LYS cc_start: 0.8589 (mttt) cc_final: 0.7737 (mmtt) REVERT: E 41 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8034 (p0) REVERT: E 77 ASN cc_start: 0.7586 (p0) cc_final: 0.7290 (p0) REVERT: I 85 MET cc_start: 0.5178 (OUTLIER) cc_final: 0.4872 (pmt) REVERT: J 33 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6747 (tt) REVERT: K 111 TYR cc_start: 0.7143 (m-80) cc_final: 0.6012 (t80) REVERT: M 45 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7960 (mttp) REVERT: L 84 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7123 (tp-100) outliers start: 79 outliers final: 55 residues processed: 255 average time/residue: 0.4351 time to fit residues: 121.8844 Evaluate side-chains 253 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 193 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 84 GLN Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 114 GLN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 87 ASN M 34 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.149123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115819 restraints weight = 14827.407| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.27 r_work: 0.3127 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11986 Z= 0.234 Angle : 0.664 9.623 16420 Z= 0.363 Chirality : 0.048 0.280 1772 Planarity : 0.004 0.040 1920 Dihedral : 16.483 155.985 1986 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 6.19 % Allowed : 29.30 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.47 (0.21), residues: 654 loop : -0.83 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 18 TYR 0.018 0.002 TYR L 97 PHE 0.037 0.002 PHE F 94 TRP 0.018 0.001 TRP I 47 HIS 0.002 0.001 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00545 (11974) covalent geometry : angle 0.66312 (16396) SS BOND : bond 0.00742 ( 12) SS BOND : angle 1.14862 ( 24) hydrogen bonds : bond 0.03662 ( 425) hydrogen bonds : angle 4.82246 ( 1077) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 196 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6886 (mp10) REVERT: B 81 GLU cc_start: 0.8004 (pp20) cc_final: 0.7596 (pp20) REVERT: C 15 LYS cc_start: 0.8624 (mttt) cc_final: 0.7787 (mmtt) REVERT: E 41 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8048 (p0) REVERT: E 77 ASN cc_start: 0.7662 (p0) cc_final: 0.7369 (p0) REVERT: J 33 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6822 (tt) REVERT: K 111 TYR cc_start: 0.7206 (m-80) cc_final: 0.6129 (t80) REVERT: M 45 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8032 (mttp) outliers start: 72 outliers final: 58 residues processed: 247 average time/residue: 0.4402 time to fit residues: 119.3564 Evaluate side-chains 254 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 109 MET Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 114 GLN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 87 ASN M 34 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.152027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119084 restraints weight = 14642.198| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.31 r_work: 0.3176 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11986 Z= 0.133 Angle : 0.582 9.146 16420 Z= 0.316 Chirality : 0.044 0.226 1772 Planarity : 0.004 0.037 1920 Dihedral : 16.242 154.083 1986 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.99 % Favored : 96.94 % Rotamer: Outliers : 4.81 % Allowed : 30.41 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.54 (0.21), residues: 654 loop : -0.69 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 18 TYR 0.015 0.001 TYR J 49 PHE 0.027 0.002 PHE F 94 TRP 0.016 0.001 TRP I 47 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00293 (11974) covalent geometry : angle 0.58229 (16396) SS BOND : bond 0.00519 ( 12) SS BOND : angle 0.71256 ( 24) hydrogen bonds : bond 0.02807 ( 425) hydrogen bonds : angle 4.54723 ( 1077) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 199 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6800 (mp10) REVERT: B 81 GLU cc_start: 0.7988 (pp20) cc_final: 0.7591 (pp20) REVERT: E 12 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7846 (m) REVERT: E 41 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7748 (p0) REVERT: E 77 ASN cc_start: 0.7514 (p0) cc_final: 0.7236 (p0) REVERT: F 53 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7722 (mmt180) REVERT: J 33 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6841 (tt) REVERT: K 111 TYR cc_start: 0.7147 (m-80) cc_final: 0.6127 (t80) REVERT: M 45 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7968 (mttp) REVERT: L 84 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7226 (tp-100) outliers start: 56 outliers final: 42 residues processed: 240 average time/residue: 0.4773 time to fit residues: 125.1262 Evaluate side-chains 242 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 84 GLN Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 88 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 114 GLN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 39 GLN K 87 ASN L 101 GLN N 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.153309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.110782 restraints weight = 14736.548| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.44 r_work: 0.3256 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11986 Z= 0.126 Angle : 0.572 9.840 16420 Z= 0.309 Chirality : 0.043 0.215 1772 Planarity : 0.004 0.038 1920 Dihedral : 16.149 154.331 1985 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % Rotamer: Outliers : 4.12 % Allowed : 31.10 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1338 helix: None (None), residues: 0 sheet: 0.62 (0.21), residues: 654 loop : -0.58 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 18 TYR 0.012 0.001 TYR A 97 PHE 0.025 0.002 PHE F 94 TRP 0.018 0.001 TRP I 47 HIS 0.001 0.000 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00278 (11974) covalent geometry : angle 0.57217 (16396) SS BOND : bond 0.00493 ( 12) SS BOND : angle 0.67755 ( 24) hydrogen bonds : bond 0.02696 ( 425) hydrogen bonds : angle 4.40116 ( 1077) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8338 (p0) cc_final: 0.8076 (p0) REVERT: A 78 GLU cc_start: 0.8639 (tt0) cc_final: 0.8269 (mm-30) REVERT: A 89 LYS cc_start: 0.8349 (mttp) cc_final: 0.8062 (mtmt) REVERT: B 81 GLU cc_start: 0.8000 (pp20) cc_final: 0.7598 (pp20) REVERT: E 12 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7866 (m) REVERT: E 41 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7556 (p0) REVERT: E 77 ASN cc_start: 0.7439 (p0) cc_final: 0.7184 (p0) REVERT: F 81 GLU cc_start: 0.8034 (pm20) cc_final: 0.7795 (pm20) REVERT: J 33 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6915 (tt) REVERT: K 111 TYR cc_start: 0.7185 (m-80) cc_final: 0.6099 (t80) REVERT: M 45 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7899 (mttp) outliers start: 48 outliers final: 37 residues processed: 232 average time/residue: 0.4417 time to fit residues: 112.0662 Evaluate side-chains 235 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 114 GLN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 39 GLN K 87 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.152352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104930 restraints weight = 14719.947| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.12 r_work: 0.3250 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11986 Z= 0.143 Angle : 0.593 9.953 16420 Z= 0.320 Chirality : 0.044 0.228 1772 Planarity : 0.004 0.039 1920 Dihedral : 16.183 154.894 1985 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.01 % Rotamer: Outliers : 3.87 % Allowed : 30.93 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.23), residues: 1338 helix: None (None), residues: 0 sheet: 0.65 (0.21), residues: 654 loop : -0.57 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 53 TYR 0.014 0.001 TYR J 49 PHE 0.027 0.002 PHE F 94 TRP 0.022 0.001 TRP I 47 HIS 0.001 0.001 HIS F 55 Details of bonding type rmsd covalent geometry : bond 0.00322 (11974) covalent geometry : angle 0.59296 (16396) SS BOND : bond 0.00548 ( 12) SS BOND : angle 0.78111 ( 24) hydrogen bonds : bond 0.02843 ( 425) hydrogen bonds : angle 4.43876 ( 1077) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4740.86 seconds wall clock time: 81 minutes 16.97 seconds (4876.97 seconds total)