Starting phenix.real_space_refine on Wed Aug 5 21:34:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tgo_55906/08_2026/9tgo_55906.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tgo_55906/08_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_55906/08_2026/9tgo_55906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tgo_55906/08_2026/9tgo_55906.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tgo_55906/08_2026/9tgo_55906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tgo_55906/08_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-2.2rc3-6140/lib/python3.11/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: 2.08, per 1000 atoms: 0.18 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: 0.58 Conformation dependent library (CDL) restraints added in 257.9 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: 1.23 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: 1.55 Time building geometry restraints manager: 0.81 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=" C2 DC S 11 " pdb=" N3 DC S 11 " ideal model delta sigma weight residual 1.353 1.385 -0.032 8.00e-03 1.56e+04 1.58e+01 bond pdb=" C3' DG O 6 " pdb=" C2' DG O 6 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG S 6 " pdb=" C2' DG S 6 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" N1 DC S 11 " pdb=" C2 DC S 11 " ideal model delta sigma weight residual 1.397 1.429 -0.032 1.00e-02 1.00e+04 9.97e+00 bond pdb=" C3' DG T 2 " pdb=" C2' DG T 2 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.12e+00 ... (remaining 11969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 16257 2.48 - 4.97: 114 4.97 - 7.45: 21 7.45 - 9.94: 3 9.94 - 12.42: 1 Bond angle restraints: 16396 Sorted by residual: angle pdb=" C2 DC S 11 " pdb=" N3 DC S 11 " pdb=" C4 DC S 11 " ideal model delta sigma weight residual 119.90 124.86 -4.96 5.00e-01 4.00e+00 9.84e+01 angle pdb=" C2 DC S 11 " pdb=" N1 DC S 11 " pdb=" C6 DC S 11 " ideal model delta sigma weight residual 120.30 123.98 -3.68 4.00e-01 6.25e+00 8.47e+01 angle pdb=" N1 DC S 11 " pdb=" C2 DC S 11 " pdb=" N3 DC S 11 " ideal model delta sigma weight residual 119.20 123.81 -4.61 7.00e-01 2.04e+00 4.33e+01 angle pdb=" O4' DG S 8 " pdb=" C4' DG S 8 " pdb=" C3' DG S 8 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.34e+01 angle pdb=" O4' DG O 8 " pdb=" C4' DG O 8 " pdb=" C3' DG O 8 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.09e+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: 1259 0.041 - 0.082: 334 0.082 - 0.123: 160 0.123 - 0.164: 13 0.164 - 0.205: 6 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.780 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:5.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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= 0.275 Angle : 0.626 12.421 16420 Z= 0.419 Chirality : 0.046 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/Z covalent geometry : bond 0.00345 / 0.27 (11974) covalent geometry : angle 0.62583 / 0.42 (16396) SS BOND : bond 0.00407 / 0.24 ( 12) SS BOND : angle 0.72078 / 0.47 ( 24) hydrogen bonds : bond 0.22208 / 14.97 ( 425) hydrogen bonds : angle 8.75590 / 6.05 ( 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 : 0.407 Fit side-chains revert: symmetry clash 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: 0.7814 (p0) REVERT: D 80 MET cc_start: 0.9297 (mmm) cc_final: 0.9017 (tpt) 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) outliers start: 34 outliers final: 12 residues processed: 273 average time/residue: 0.4076 time to fit residues: 121.8184 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 : 0.249 ------------------------------------------------------------------------------- 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: 9.9990 chunk 107 optimal weight: 0.4980 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: 8.9990 chunk 55 optimal weight: 2.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN C 28 ASN C 39 GLN E 38 GLN D 3 GLN D 84 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 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 = 0.3988 r_free = 0.3988 target = 0.153897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120481 restraints weight = 14152.877| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.28 r_work: 0.3182 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11986 Z= 0.287 Angle : 0.730 9.216 16420 Z= 0.410 Chirality : 0.054 0.513 1772 Planarity : 0.005 0.041 1920 Dihedral : 16.372 148.220 2000 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.99 % Favored : 96.86 % Rotamer: Outliers : 8.16 % Allowed : 27.58 % Favored : 64.26 % 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: -0.56 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.26 (0.21), residues: 654 loop : -0.99 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 18 TYR 0.027 0.002 TYR L 97 PHE 0.045 0.003 PHE F 94 TRP 0.012 0.002 TRP I 47 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.29 (11974) covalent geometry : angle 0.72859 / 0.41 (16396) SS BOND : bond 0.00789 / 0.46 ( 12) SS BOND : angle 1.38203 / 0.91 ( 24) hydrogen bonds : bond 0.05111 / 3.44 ( 425) hydrogen bonds : angle 5.95577 / 4.13 ( 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 295 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 200 time to evaluate : 0.324 Fit side-chains REVERT: A 1 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8046 (ptmt) REVERT: B 81 GLU cc_start: 0.7816 (pp20) cc_final: 0.7454 (pp20) REVERT: C 3 GLN cc_start: 0.8490 (mt0) cc_final: 0.8140 (mm-40) REVERT: C 15 LYS cc_start: 0.8733 (mttt) cc_final: 0.8089 (mmtt) REVERT: E 12 SER cc_start: 0.8352 (OUTLIER) cc_final: 0.8053 (m) REVERT: E 41 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8204 (p0) REVERT: E 77 ASN cc_start: 0.7777 (p0) cc_final: 0.7370 (p0) REVERT: I 85 MET cc_start: 0.5342 (OUTLIER) cc_final: 0.5097 (pmt) REVERT: I 100 ARG cc_start: 0.7076 (tmm160) cc_final: 0.6622 (ttp80) REVERT: I 110 ASP cc_start: 0.5103 (OUTLIER) cc_final: 0.4824 (p0) REVERT: J 33 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7185 (tp) REVERT: K 86 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8277 (pp) REVERT: K 111 TYR cc_start: 0.7427 (m-80) cc_final: 0.6567 (t80) REVERT: N 11 LEU cc_start: 0.5175 (OUTLIER) cc_final: 0.4647 (tm) REVERT: N 65 SER cc_start: 0.7372 (OUTLIER) cc_final: 0.7072 (p) outliers start: 95 outliers final: 38 residues processed: 266 average time/residue: 0.3861 time to fit residues: 113.3198 Evaluate side-chains 239 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 71 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 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 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 F residue 54 LEU 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 106 ILE 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 86 ILE Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 69 THR 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 11 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 74 THR 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: 0.9980 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN E 6 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 3 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.155463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122413 restraints weight = 14238.410| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.21 r_work: 0.3215 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11986 Z= 0.150 Angle : 0.602 7.313 16420 Z= 0.343 Chirality : 0.049 0.402 1772 Planarity : 0.004 0.036 1920 Dihedral : 16.392 149.443 1989 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.99 % Favored : 96.86 % Rotamer: Outliers : 5.84 % Allowed : 28.78 % Favored : 65.38 % 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: -0.43 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.32 (0.21), residues: 654 loop : -0.87 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 18 TYR 0.018 0.001 TYR L 97 PHE 0.028 0.002 PHE F 94 TRP 0.009 0.001 TRP D 47 HIS 0.001 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (11974) covalent geometry : angle 0.60128 / 0.34 (16396) SS BOND : bond 0.00610 / 0.41 ( 12) SS BOND : angle 0.92232 / 0.63 ( 24) hydrogen bonds : bond 0.03846 / 2.57 ( 425) hydrogen bonds : angle 5.43883 / 3.78 ( 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 262 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 194 time to evaluate : 0.306 Fit side-chains REVERT: A 1 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8042 (ptmt) REVERT: B 81 GLU cc_start: 0.7787 (pp20) cc_final: 0.7447 (pp20) REVERT: C 3 GLN cc_start: 0.8466 (mt0) cc_final: 0.8149 (mm-40) REVERT: C 15 LYS cc_start: 0.8743 (mttt) cc_final: 0.8115 (mmtt) REVERT: E 12 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.8038 (m) REVERT: E 41 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8041 (p0) REVERT: E 77 ASN cc_start: 0.7753 (p0) cc_final: 0.7395 (p0) REVERT: I 85 MET cc_start: 0.5389 (OUTLIER) cc_final: 0.5095 (pmt) REVERT: J 33 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7021 (tp) REVERT: K 111 TYR cc_start: 0.7381 (m-80) cc_final: 0.6570 (t80) REVERT: M 3 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: N 11 LEU cc_start: 0.5212 (OUTLIER) cc_final: 0.4707 (tm) outliers start: 68 outliers final: 32 residues processed: 238 average time/residue: 0.3732 time to fit residues: 97.7368 Evaluate side-chains 230 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS Chi-restraints excluded: chain B residue 15 LEU 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 E residue 41 ASP Chi-restraints excluded: chain E residue 74 THR 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 63 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 85 MET 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 69 THR Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 73 SER 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 37 optimal weight: 3.9990 chunk 115 optimal weight: 0.0870 chunk 128 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 0.1980 chunk 113 optimal weight: 9.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 114 GLN B 31 ASN C 87 ASN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 87 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 = 0.4012 r_free = 0.4012 target = 0.156163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.122440 restraints weight = 14220.173| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.51 r_work: 0.3209 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11986 Z= 0.134 Angle : 0.588 7.454 16420 Z= 0.333 Chirality : 0.047 0.389 1772 Planarity : 0.004 0.036 1920 Dihedral : 16.334 148.455 1988 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.69 % Favored : 97.16 % Rotamer: Outliers : 5.41 % Allowed : 29.04 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.26 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.44 (0.20), residues: 654 loop : -0.76 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 18 TYR 0.015 0.001 TYR L 97 PHE 0.026 0.002 PHE F 94 TRP 0.009 0.001 TRP D 47 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (11974) covalent geometry : angle 0.58664 / 0.33 (16396) SS BOND : bond 0.00604 / 0.38 ( 12) SS BOND : angle 1.23210 / 0.75 ( 24) hydrogen bonds : bond 0.03314 / 2.21 ( 425) hydrogen bonds : angle 5.08472 / 3.55 ( 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 252 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 189 time to evaluate : 0.296 Fit side-chains REVERT: A 1 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8008 (ptmt) REVERT: B 81 GLU cc_start: 0.7801 (pp20) cc_final: 0.7472 (pp20) REVERT: C 3 GLN cc_start: 0.8456 (mt0) cc_final: 0.8122 (mm-40) REVERT: C 15 LYS cc_start: 0.8726 (mttt) cc_final: 0.8094 (mmtt) REVERT: E 12 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8026 (m) REVERT: E 41 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7925 (p0) REVERT: E 77 ASN cc_start: 0.7699 (p0) cc_final: 0.7384 (p0) REVERT: D 95 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8649 (ttp) REVERT: I 71 THR cc_start: 0.5484 (OUTLIER) cc_final: 0.5027 (t) REVERT: I 85 MET cc_start: 0.5370 (OUTLIER) cc_final: 0.5064 (pmt) REVERT: J 33 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7115 (tt) REVERT: K 111 TYR cc_start: 0.7400 (m-80) cc_final: 0.6463 (t80) REVERT: M 3 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: N 11 LEU cc_start: 0.5104 (OUTLIER) cc_final: 0.4615 (tm) outliers start: 63 outliers final: 35 residues processed: 232 average time/residue: 0.4008 time to fit residues: 102.2549 Evaluate side-chains 233 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 41 ASP Chi-restraints excluded: chain E residue 85 THR 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 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 97 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 71 THR 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 69 THR Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 8 ILE 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 33 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 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: 8.9990 chunk 116 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 14 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 = 0.3985 r_free = 0.3985 target = 0.153991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120615 restraints weight = 14295.119| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.19 r_work: 0.3185 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 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 = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11986 Z= 0.199 Angle : 0.649 8.954 16420 Z= 0.366 Chirality : 0.051 0.476 1772 Planarity : 0.004 0.037 1920 Dihedral : 16.317 147.752 1988 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 6.27 % Allowed : 27.49 % Favored : 66.24 % 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: -0.22 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.49 (0.21), residues: 654 loop : -0.76 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 50 TYR 0.020 0.002 TYR L 97 PHE 0.039 0.002 PHE F 94 TRP 0.011 0.001 TRP D 47 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (11974) covalent geometry : angle 0.64544 / 0.37 (16396) SS BOND : bond 0.00805 / 0.52 ( 12) SS BOND : angle 1.79371 / 0.97 ( 24) hydrogen bonds : bond 0.03982 / 2.67 ( 425) hydrogen bonds : angle 4.94578 / 3.42 ( 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 268 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 195 time to evaluate : 0.440 Fit side-chains REVERT: A 1 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8022 (ptmm) REVERT: B 81 GLU cc_start: 0.7808 (pp20) cc_final: 0.7492 (pp20) REVERT: C 3 GLN cc_start: 0.8502 (mt0) cc_final: 0.8080 (mm-40) REVERT: C 15 LYS cc_start: 0.8735 (mttt) cc_final: 0.8093 (mmtt) REVERT: E 12 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.7963 (m) REVERT: E 41 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8048 (p0) REVERT: E 77 ASN cc_start: 0.7757 (p0) cc_final: 0.7416 (p0) REVERT: D 95 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8609 (tpp) REVERT: I 80 MET cc_start: 0.5978 (mmm) cc_final: 0.5726 (mmm) REVERT: I 85 MET cc_start: 0.5339 (OUTLIER) cc_final: 0.5062 (pmt) REVERT: J 33 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7180 (tp) REVERT: K 111 TYR cc_start: 0.7531 (m-80) cc_final: 0.6546 (t80) REVERT: M 3 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: N 11 LEU cc_start: 0.5082 (OUTLIER) cc_final: 0.4634 (tm) outliers start: 73 outliers final: 45 residues processed: 249 average time/residue: 0.4049 time to fit residues: 110.9813 Evaluate side-chains 243 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 27 GLN 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 74 THR Chi-restraints excluded: chain E residue 85 THR 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 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 I residue 5 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 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 3 GLN Chi-restraints excluded: chain K residue 73 SER 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 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 8 ILE Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 11 LEU 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 74 THR 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: 7.9990 chunk 10 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 114 GLN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 39 GLN K 87 ASN M 34 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.121855 restraints weight = 14281.275| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.06 r_work: 0.3184 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 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 = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11986 Z= 0.188 Angle : 0.629 8.245 16420 Z= 0.356 Chirality : 0.050 0.447 1772 Planarity : 0.004 0.040 1920 Dihedral : 16.346 148.103 1988 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.01 % Rotamer: Outliers : 5.33 % Allowed : 28.61 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.18 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.50 (0.20), residues: 654 loop : -0.72 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 18 TYR 0.018 0.002 TYR L 97 PHE 0.033 0.002 PHE F 94 TRP 0.010 0.001 TRP D 47 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (11974) covalent geometry : angle 0.62767 / 0.36 (16396) SS BOND : bond 0.00686 / 0.45 ( 12) SS BOND : angle 1.40098 / 0.82 ( 24) hydrogen bonds : bond 0.03757 / 2.52 ( 425) hydrogen bonds : angle 4.88740 / 3.39 ( 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 250 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: B 81 GLU cc_start: 0.7846 (pp20) cc_final: 0.7521 (pp20) REVERT: C 15 LYS cc_start: 0.8705 (mttt) cc_final: 0.8036 (mmtt) REVERT: E 12 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7939 (m) REVERT: E 41 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8040 (p0) REVERT: E 77 ASN cc_start: 0.7747 (p0) cc_final: 0.7424 (p0) REVERT: D 95 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8605 (tpp) REVERT: I 66 MET cc_start: 0.5260 (mpp) cc_final: 0.4984 (mtt) REVERT: I 80 MET cc_start: 0.5855 (mmm) cc_final: 0.5563 (mmm) REVERT: I 85 MET cc_start: 0.5342 (OUTLIER) cc_final: 0.5058 (pmt) REVERT: J 33 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7161 (tp) REVERT: K 111 TYR cc_start: 0.7529 (m-80) cc_final: 0.6494 (t80) REVERT: M 3 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: N 11 LEU cc_start: 0.4961 (OUTLIER) cc_final: 0.4563 (tm) outliers start: 62 outliers final: 44 residues processed: 231 average time/residue: 0.3849 time to fit residues: 97.9523 Evaluate side-chains 238 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN 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 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 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 3 GLN Chi-restraints excluded: chain K residue 73 SER 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 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 11 LEU 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 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: 20.0000 chunk 84 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.152405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.119071 restraints weight = 14300.668| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.16 r_work: 0.3165 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- 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 = 0.01 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 = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11986 Z= 0.267 Angle : 0.696 9.479 16420 Z= 0.391 Chirality : 0.053 0.518 1772 Planarity : 0.004 0.050 1920 Dihedral : 16.392 147.240 1988 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.44 % Favored : 96.49 % Rotamer: Outliers : 6.01 % Allowed : 27.41 % Favored : 66.58 % 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: -0.25 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.49 (0.20), residues: 654 loop : -0.80 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 38 TYR 0.022 0.002 TYR L 97 PHE 0.039 0.003 PHE F 94 TRP 0.011 0.002 TRP I 47 HIS 0.003 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.27 (11974) covalent geometry : angle 0.69321 / 0.39 (16396) SS BOND : bond 0.00831 / 0.54 ( 12) SS BOND : angle 1.69892 / 1.00 ( 24) hydrogen bonds : bond 0.04347 / 2.92 ( 425) hydrogen bonds : angle 4.95345 / 3.43 ( 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 263 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: B 81 GLU cc_start: 0.7882 (pp20) cc_final: 0.7535 (pp20) REVERT: C 15 LYS cc_start: 0.8710 (mttt) cc_final: 0.8028 (mmtt) REVERT: E 12 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7840 (m) REVERT: E 41 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8177 (p0) REVERT: E 77 ASN cc_start: 0.7843 (p0) cc_final: 0.7474 (p0) REVERT: D 95 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8642 (ttp) REVERT: I 66 MET cc_start: 0.5263 (mpp) cc_final: 0.5053 (mtt) REVERT: I 85 MET cc_start: 0.5235 (OUTLIER) cc_final: 0.4960 (pmt) REVERT: J 33 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7171 (tp) REVERT: K 111 TYR cc_start: 0.7599 (m-80) cc_final: 0.6563 (t80) REVERT: M 3 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: N 11 LEU cc_start: 0.4887 (OUTLIER) cc_final: 0.4527 (tm) outliers start: 70 outliers final: 50 residues processed: 243 average time/residue: 0.3738 time to fit residues: 99.9327 Evaluate side-chains 247 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 17 ASP 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 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 J residue 12 SER 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 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 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 85 MET 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 11 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 74 THR 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: 1.9990 chunk 100 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 114 GLN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 39 GLN K 87 ASN M 34 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.154629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121339 restraints weight = 14274.241| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.27 r_work: 0.3194 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11986 Z= 0.138 Angle : 0.598 8.800 16420 Z= 0.338 Chirality : 0.048 0.378 1772 Planarity : 0.004 0.037 1920 Dihedral : 16.367 148.766 1988 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 4.73 % Allowed : 29.04 % Favored : 66.24 % 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: -0.12 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.55 (0.21), residues: 654 loop : -0.67 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 50 TYR 0.016 0.001 TYR J 49 PHE 0.027 0.002 PHE E 94 TRP 0.012 0.001 TRP I 47 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (11974) covalent geometry : angle 0.59744 / 0.34 (16396) SS BOND : bond 0.00555 / 0.36 ( 12) SS BOND : angle 0.99919 / 0.62 ( 24) hydrogen bonds : bond 0.03284 / 2.21 ( 425) hydrogen bonds : angle 4.79797 / 3.33 ( 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 239 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 0.389 Fit side-chains REVERT: B 81 GLU cc_start: 0.7872 (pp20) cc_final: 0.7529 (pp20) REVERT: C 15 LYS cc_start: 0.8707 (mttt) cc_final: 0.8031 (mmtt) REVERT: E 12 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7859 (m) REVERT: E 41 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7997 (p0) REVERT: E 77 ASN cc_start: 0.7721 (p0) cc_final: 0.7435 (p0) REVERT: D 95 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8623 (ttp) REVERT: F 53 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7911 (mmt180) REVERT: I 66 MET cc_start: 0.5190 (mpp) cc_final: 0.4798 (mtt) REVERT: I 85 MET cc_start: 0.5349 (OUTLIER) cc_final: 0.5119 (pmt) REVERT: J 33 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7142 (tp) REVERT: K 111 TYR cc_start: 0.7484 (m-80) cc_final: 0.6468 (t80) REVERT: M 3 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8116 (mt0) outliers start: 55 outliers final: 39 residues processed: 223 average time/residue: 0.3927 time to fit residues: 96.1179 Evaluate side-chains 226 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain E residue 12 SER 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 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 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 69 THR Chi-restraints excluded: chain K residue 73 SER 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 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 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 33 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 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: 9.9990 chunk 97 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 0.0060 chunk 91 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 114 GLN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 87 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.154878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121753 restraints weight = 14151.743| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.28 r_work: 0.3202 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2473 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= 0.140 Angle : 0.595 8.913 16420 Z= 0.335 Chirality : 0.048 0.396 1772 Planarity : 0.004 0.040 1920 Dihedral : 16.228 147.380 1986 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % Rotamer: Outliers : 4.30 % Allowed : 29.73 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.59 (0.21), residues: 654 loop : -0.60 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 18 TYR 0.016 0.001 TYR J 49 PHE 0.029 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/Z covalent geometry : bond 0.00285 / 0.14 (11974) covalent geometry : angle 0.59395 / 0.33 (16396) SS BOND : bond 0.00604 / 0.40 ( 12) SS BOND : angle 1.00118 / 0.61 ( 24) hydrogen bonds : bond 0.03177 / 2.13 ( 425) hydrogen bonds : angle 4.64865 / 3.24 ( 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 236 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.329 Fit side-chains REVERT: B 81 GLU cc_start: 0.7865 (pp20) cc_final: 0.7528 (pp20) REVERT: C 15 LYS cc_start: 0.8692 (mttt) cc_final: 0.8015 (mmtt) REVERT: E 12 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.7897 (m) REVERT: E 41 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7933 (p0) REVERT: E 77 ASN cc_start: 0.7717 (p0) cc_final: 0.7457 (p0) REVERT: D 95 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8540 (tpp) REVERT: I 85 MET cc_start: 0.5420 (OUTLIER) cc_final: 0.5195 (pmt) REVERT: J 33 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6984 (tt) REVERT: K 111 TYR cc_start: 0.7502 (m-80) cc_final: 0.6467 (t80) REVERT: M 3 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8131 (mt0) outliers start: 50 outliers final: 38 residues processed: 220 average time/residue: 0.3660 time to fit residues: 88.5749 Evaluate side-chains 226 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 7 SER Chi-restraints excluded: chain E residue 12 SER 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 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 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 69 THR Chi-restraints excluded: chain K residue 73 SER 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 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 33 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 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: 20.0000 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.154330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.121066 restraints weight = 14287.776| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.28 r_work: 0.3189 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 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 = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11986 Z= 0.157 Angle : 0.610 9.460 16420 Z= 0.343 Chirality : 0.048 0.411 1772 Planarity : 0.004 0.039 1920 Dihedral : 16.218 147.397 1986 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.99 % Favored : 96.94 % Rotamer: Outliers : 4.30 % Allowed : 29.81 % Favored : 65.89 % 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: -0.00 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.60 (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 I 50 TYR 0.015 0.001 TYR L 97 PHE 0.031 0.002 PHE F 94 TRP 0.023 0.001 TRP I 47 HIS 0.001 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (11974) covalent geometry : angle 0.60911 / 0.34 (16396) SS BOND : bond 0.00628 / 0.41 ( 12) SS BOND : angle 1.09222 / 0.67 ( 24) hydrogen bonds : bond 0.03336 / 2.24 ( 425) hydrogen bonds : angle 4.63042 / 3.23 ( 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 237 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.332 Fit side-chains REVERT: B 81 GLU cc_start: 0.7872 (pp20) cc_final: 0.7522 (pp20) REVERT: C 15 LYS cc_start: 0.8686 (mttt) cc_final: 0.8009 (mmtt) REVERT: C 78 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8085 (mm-30) REVERT: E 12 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.7892 (m) REVERT: E 41 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7943 (p0) REVERT: E 77 ASN cc_start: 0.7713 (p0) cc_final: 0.7458 (p0) REVERT: D 95 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8559 (tpp) REVERT: I 85 MET cc_start: 0.5336 (OUTLIER) cc_final: 0.5003 (pmt) REVERT: J 33 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6975 (tt) REVERT: K 111 TYR cc_start: 0.7514 (m-80) cc_final: 0.6491 (t80) outliers start: 50 outliers final: 38 residues processed: 221 average time/residue: 0.4217 time to fit residues: 102.4058 Evaluate side-chains 228 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain E residue 12 SER 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 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 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 69 THR 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 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 33 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 60 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 95 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 2 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.152555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118892 restraints weight = 14313.065| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.25 r_work: 0.3171 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 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 = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11986 Z= 0.232 Angle : 0.678 9.726 16420 Z= 0.379 Chirality : 0.052 0.487 1772 Planarity : 0.004 0.040 1920 Dihedral : 16.257 146.781 1986 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 4.04 % Allowed : 30.15 % Favored : 65.81 % 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: -0.11 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.56 (0.21), residues: 654 loop : -0.68 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 53 TYR 0.020 0.002 TYR L 97 PHE 0.039 0.002 PHE F 94 TRP 0.023 0.002 TRP I 47 HIS 0.003 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (11974) covalent geometry : angle 0.67646 / 0.38 (16396) SS BOND : bond 0.00790 / 0.52 ( 12) SS BOND : angle 1.49321 / 0.89 ( 24) hydrogen bonds : bond 0.04009 / 2.70 ( 425) hydrogen bonds : angle 4.76897 / 3.33 ( 1077) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3748.60 seconds wall clock time: 64 minutes 21.70 seconds (3861.70 seconds total)