Starting phenix.real_space_refine on Fri Jul 3 03:30:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tgo_55906/07_2026/9tgo_55906.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tgo_55906/07_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_55906/07_2026/9tgo_55906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tgo_55906/07_2026/9tgo_55906.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tgo_55906/07_2026/9tgo_55906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tgo_55906/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.59, per 1000 atoms: 0.22 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: 0.67 Conformation dependent library (CDL) restraints added in 306.5 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: 1.33 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: 1.87 Time building geometry restraints manager: 0.93 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: 3.470 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: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.820 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- 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 : 0.624 12.421 16420 Z= 0.416 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 0.62386 / 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 : 0.403 Fit side-chains revert: symmetry clash REVERT: C 3 GLN cc_start: 0.8817 (mt0) cc_final: 0.8536 (mm-40) REVERT: E 45 LYS cc_start: 0.8444 (mtpm) cc_final: 0.8205 (mttm) REVERT: E 77 ASN cc_start: 0.8059 (p0) cc_final: 0.7815 (p0) REVERT: D 80 MET cc_start: 0.9297 (mmm) cc_final: 0.9017 (tpt) REVERT: K 17 SER cc_start: 0.7838 (m) cc_final: 0.7638 (m) REVERT: K 111 TYR cc_start: 0.7663 (m-80) cc_final: 0.7026 (t80) REVERT: N 11 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5896 (tm) REVERT: N 53 ARG cc_start: 0.6740 (mtt180) cc_final: 0.6491 (mmm-85) outliers start: 34 outliers final: 12 residues processed: 273 average time/residue: 0.4500 time to fit residues: 134.2413 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 : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 44 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 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: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.154582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121910 restraints weight = 14117.938| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.15 r_work: 0.3187 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 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 = 0.3166 r_free = 0.3166 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: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11986 Z= 0.246 Angle : 0.699 8.590 16420 Z= 0.394 Chirality : 0.053 0.474 1772 Planarity : 0.005 0.039 1920 Dihedral : 16.325 147.971 2000 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.99 % Favored : 96.86 % Rotamer: Outliers : 7.90 % Allowed : 27.66 % Favored : 64.43 % 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: 0.25 (0.21), residues: 654 loop : -0.97 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 18 TYR 0.025 0.002 TYR L 97 PHE 0.044 0.003 PHE F 94 TRP 0.011 0.002 TRP A 47 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.25 (11974) covalent geometry : angle 0.69818 / 0.39 (16396) SS BOND : bond 0.00693 / 0.40 ( 12) SS BOND : angle 1.27103 / 0.84 ( 24) hydrogen bonds : bond 0.04817 / 3.24 ( 425) hydrogen bonds : angle 5.86300 / 4.05 ( 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 296 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 204 time to evaluate : 0.457 Fit side-chains REVERT: A 1 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8018 (ptmt) REVERT: B 81 GLU cc_start: 0.7810 (pp20) cc_final: 0.7455 (pp20) REVERT: C 3 GLN cc_start: 0.8476 (mt0) cc_final: 0.8144 (mm-40) REVERT: C 15 LYS cc_start: 0.8723 (mttt) cc_final: 0.8078 (mmtt) REVERT: E 12 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.8052 (m) REVERT: E 41 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8123 (p0) REVERT: E 77 ASN cc_start: 0.7753 (p0) cc_final: 0.7358 (p0) REVERT: I 85 MET cc_start: 0.5359 (OUTLIER) cc_final: 0.5111 (pmt) REVERT: I 100 ARG cc_start: 0.7093 (tmm160) cc_final: 0.6636 (ttp80) REVERT: I 110 ASP cc_start: 0.5077 (OUTLIER) cc_final: 0.4810 (p0) REVERT: J 33 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7192 (tp) REVERT: K 111 TYR cc_start: 0.7400 (m-80) cc_final: 0.6558 (t80) REVERT: N 11 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4684 (tm) REVERT: N 65 SER cc_start: 0.7368 (OUTLIER) cc_final: 0.7077 (p) outliers start: 92 outliers final: 35 residues processed: 267 average time/residue: 0.4538 time to fit residues: 133.6358 Evaluate side-chains 238 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 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 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 3 GLN Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 19 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: 0.6980 chunk 5 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 39 GLN K 87 ASN L 3 GLN L 101 GLN N 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.156186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123263 restraints weight = 14268.218| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.20 r_work: 0.3217 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 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 = 0.3199 r_free = 0.3199 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: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11986 Z= 0.143 Angle : 0.589 6.841 16420 Z= 0.336 Chirality : 0.047 0.358 1772 Planarity : 0.004 0.036 1920 Dihedral : 16.331 148.736 1988 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.06 % Favored : 96.79 % Rotamer: Outliers : 6.10 % Allowed : 28.78 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.36 (0.20), residues: 654 loop : -0.83 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 18 TYR 0.017 0.001 TYR L 97 PHE 0.025 0.002 PHE E 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 0.00286 / 0.14 (11974) covalent geometry : angle 0.58724 / 0.34 (16396) SS BOND : bond 0.00775 / 0.46 ( 12) SS BOND : angle 1.17007 / 0.68 ( 24) hydrogen bonds : bond 0.03673 / 2.44 ( 425) hydrogen bonds : angle 5.35517 / 3.73 ( 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 263 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 192 time to evaluate : 0.428 Fit side-chains REVERT: B 81 GLU cc_start: 0.7818 (pp20) cc_final: 0.7469 (pp20) REVERT: C 3 GLN cc_start: 0.8468 (mt0) cc_final: 0.8157 (mm-40) REVERT: C 15 LYS cc_start: 0.8735 (mttt) cc_final: 0.8101 (mmtt) REVERT: E 12 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.8040 (m) REVERT: E 41 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8015 (p0) REVERT: E 77 ASN cc_start: 0.7736 (p0) cc_final: 0.7369 (p0) REVERT: D 95 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8654 (ttp) REVERT: I 71 THR cc_start: 0.5376 (OUTLIER) cc_final: 0.4950 (t) REVERT: I 85 MET cc_start: 0.5384 (OUTLIER) cc_final: 0.5104 (pmt) REVERT: J 33 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7038 (tp) REVERT: K 111 TYR cc_start: 0.7401 (m-80) cc_final: 0.6575 (t80) REVERT: M 3 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8032 (mt0) REVERT: N 11 LEU cc_start: 0.5189 (OUTLIER) cc_final: 0.4675 (tm) outliers start: 71 outliers final: 34 residues processed: 238 average time/residue: 0.4779 time to fit residues: 125.0722 Evaluate side-chains 233 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 THR Chi-restraints excluded: chain E residue 85 THR 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 F residue 106 ILE Chi-restraints excluded: chain I residue 53 SER 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 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 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 44 VAL 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 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 37 optimal weight: 0.8980 chunk 115 optimal weight: 0.0470 chunk 128 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 23 optimal weight: 0.0870 chunk 69 optimal weight: 0.0770 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 overall best weight: 0.8216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN B 31 ASN C 87 ASN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.156891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.123677 restraints weight = 14227.942| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.20 r_work: 0.3233 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11986 Z= 0.125 Angle : 0.572 7.157 16420 Z= 0.325 Chirality : 0.046 0.346 1772 Planarity : 0.004 0.036 1920 Dihedral : 16.253 147.455 1988 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 4.12 % Allowed : 30.33 % 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: -0.21 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.47 (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 0.017 0.001 TYR J 49 PHE 0.024 0.002 PHE F 94 TRP 0.008 0.001 TRP D 47 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (11974) covalent geometry : angle 0.56937 / 0.32 (16396) SS BOND : bond 0.00698 / 0.39 ( 12) SS BOND : angle 1.53361 / 0.80 ( 24) hydrogen bonds : bond 0.03155 / 2.11 ( 425) hydrogen bonds : angle 5.00340 / 3.48 ( 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 240 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 0.495 Fit side-chains REVERT: A 1 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8036 (ptmt) REVERT: B 81 GLU cc_start: 0.7805 (pp20) cc_final: 0.7479 (pp20) REVERT: C 3 GLN cc_start: 0.8448 (mt0) cc_final: 0.8137 (mm-40) REVERT: C 15 LYS cc_start: 0.8722 (mttt) cc_final: 0.8089 (mmtt) REVERT: E 12 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.8023 (m) REVERT: E 77 ASN cc_start: 0.7632 (p0) cc_final: 0.7325 (p0) REVERT: D 95 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8648 (ttp) REVERT: I 85 MET cc_start: 0.5360 (OUTLIER) cc_final: 0.5053 (pmt) REVERT: J 33 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7161 (tt) REVERT: K 111 TYR cc_start: 0.7419 (m-80) cc_final: 0.6519 (t80) REVERT: M 3 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: M 4 MET cc_start: 0.8425 (mmm) cc_final: 0.8202 (mmp) REVERT: N 11 LEU cc_start: 0.5166 (OUTLIER) cc_final: 0.4672 (tm) outliers start: 48 outliers final: 30 residues processed: 225 average time/residue: 0.4401 time to fit residues: 108.8112 Evaluate side-chains 225 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 97 THR Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 85 MET Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 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 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 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 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: 4.9990 chunk 106 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 14 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 39 GLN K 87 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121625 restraints weight = 14310.556| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.04 r_work: 0.3187 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 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 (3 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11986 Z= 0.206 Angle : 0.647 8.491 16420 Z= 0.367 Chirality : 0.051 0.453 1772 Planarity : 0.004 0.037 1920 Dihedral : 16.249 147.050 1988 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 6.01 % Allowed : 28.18 % 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: -0.21 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.50 (0.20), residues: 654 loop : -0.76 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 18 TYR 0.020 0.002 TYR L 97 PHE 0.040 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 0.00453 / 0.21 (11974) covalent geometry : angle 0.64476 / 0.37 (16396) SS BOND : bond 0.00793 / 0.51 ( 12) SS BOND : angle 1.60150 / 0.93 ( 24) hydrogen bonds : bond 0.04047 / 2.71 ( 425) hydrogen bonds : angle 4.94488 / 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 263 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 0.423 Fit side-chains REVERT: A 1 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8010 (ptmm) REVERT: B 81 GLU cc_start: 0.7809 (pp20) cc_final: 0.7470 (pp20) REVERT: C 3 GLN cc_start: 0.8501 (mt0) cc_final: 0.8075 (mm-40) REVERT: C 15 LYS cc_start: 0.8718 (mttt) cc_final: 0.8066 (mmtt) REVERT: E 12 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.7984 (m) REVERT: E 41 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8045 (p0) REVERT: E 77 ASN cc_start: 0.7739 (p0) cc_final: 0.7392 (p0) REVERT: D 95 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8608 (tpp) REVERT: I 85 MET cc_start: 0.5357 (OUTLIER) cc_final: 0.5089 (pmt) REVERT: J 33 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7160 (tp) REVERT: K 111 TYR cc_start: 0.7529 (m-80) cc_final: 0.6522 (t80) REVERT: M 3 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8034 (mt0) REVERT: N 11 LEU cc_start: 0.4991 (OUTLIER) cc_final: 0.4539 (tm) outliers start: 70 outliers final: 44 residues processed: 244 average time/residue: 0.4513 time to fit residues: 121.0602 Evaluate side-chains 238 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.2980 chunk 10 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 79 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.155130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.122155 restraints weight = 14248.266| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.17 r_work: 0.3201 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11986 Z= 0.146 Angle : 0.591 7.490 16420 Z= 0.337 Chirality : 0.048 0.373 1772 Planarity : 0.004 0.036 1920 Dihedral : 16.260 147.542 1988 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.01 % Rotamer: Outliers : 4.81 % Allowed : 29.30 % 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: -0.12 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.54 (0.20), residues: 654 loop : -0.66 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 18 TYR 0.016 0.001 TYR L 97 PHE 0.028 0.002 PHE F 94 TRP 0.010 0.001 TRP D 47 HIS 0.001 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (11974) covalent geometry : angle 0.58976 / 0.34 (16396) SS BOND : bond 0.00606 / 0.39 ( 12) SS BOND : angle 1.11094 / 0.68 ( 24) hydrogen bonds : bond 0.03416 / 2.29 ( 425) hydrogen bonds : angle 4.83468 / 3.35 ( 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 240 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.321 Fit side-chains REVERT: A 1 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8002 (ptmm) REVERT: B 81 GLU cc_start: 0.7848 (pp20) cc_final: 0.7509 (pp20) REVERT: C 3 GLN cc_start: 0.8502 (mt0) cc_final: 0.8069 (mm-40) REVERT: C 15 LYS cc_start: 0.8715 (mttt) cc_final: 0.8059 (mmtt) REVERT: E 12 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.7986 (m) REVERT: E 41 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7987 (p0) REVERT: E 77 ASN cc_start: 0.7702 (p0) cc_final: 0.7420 (p0) REVERT: D 95 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8639 (ttp) REVERT: I 85 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.5145 (pmt) REVERT: J 33 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7150 (tp) REVERT: K 111 TYR cc_start: 0.7478 (m-80) cc_final: 0.6497 (t80) REVERT: M 3 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: N 11 LEU cc_start: 0.5041 (OUTLIER) cc_final: 0.4589 (tm) outliers start: 56 outliers final: 38 residues processed: 224 average time/residue: 0.4421 time to fit residues: 108.7551 Evaluate side-chains 228 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LYS 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 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 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 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 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 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 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 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: 10.0000 chunk 84 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.153099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120222 restraints weight = 14290.220| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.13 r_work: 0.3176 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 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: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11986 Z= 0.246 Angle : 0.668 8.786 16420 Z= 0.377 Chirality : 0.052 0.464 1772 Planarity : 0.004 0.037 1920 Dihedral : 16.291 146.448 1988 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.21 % Favored : 96.71 % Rotamer: Outliers : 5.76 % Allowed : 28.44 % 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: -0.18 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.52 (0.20), residues: 654 loop : -0.74 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 18 TYR 0.020 0.002 TYR L 97 PHE 0.040 0.003 PHE F 94 TRP 0.011 0.002 TRP D 47 HIS 0.002 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.25 (11974) covalent geometry : angle 0.66572 / 0.38 (16396) SS BOND : bond 0.00778 / 0.51 ( 12) SS BOND : angle 1.50999 / 0.92 ( 24) hydrogen bonds : bond 0.04129 / 2.77 ( 425) hydrogen bonds : angle 4.91045 / 3.41 ( 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 253 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 0.455 Fit side-chains REVERT: B 81 GLU cc_start: 0.7882 (pp20) cc_final: 0.7527 (pp20) REVERT: C 15 LYS cc_start: 0.8716 (mttt) cc_final: 0.8031 (mmtt) REVERT: E 12 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.7849 (m) REVERT: E 41 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8104 (p0) REVERT: E 77 ASN cc_start: 0.7784 (p0) cc_final: 0.7433 (p0) REVERT: D 95 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8627 (tpp) REVERT: I 66 MET cc_start: 0.5307 (mpp) cc_final: 0.5046 (mtt) REVERT: I 85 MET cc_start: 0.5340 (OUTLIER) cc_final: 0.5081 (pmt) REVERT: J 26 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.7738 (m) REVERT: J 33 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7164 (tp) REVERT: K 111 TYR cc_start: 0.7570 (m-80) cc_final: 0.6534 (t80) REVERT: M 3 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: N 11 LEU cc_start: 0.4994 (OUTLIER) cc_final: 0.4618 (tm) outliers start: 67 outliers final: 47 residues processed: 234 average time/residue: 0.4189 time to fit residues: 107.6846 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 : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 12 VAL Chi-restraints excluded: chain C residue 64 ASP 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.154995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.121640 restraints weight = 14264.256| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.27 r_work: 0.3196 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11986 Z= 0.136 Angle : 0.590 9.009 16420 Z= 0.335 Chirality : 0.047 0.354 1772 Planarity : 0.004 0.037 1920 Dihedral : 16.269 147.310 1988 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.01 % Rotamer: Outliers : 4.47 % Allowed : 29.55 % 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: -0.07 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.55 (0.20), residues: 654 loop : -0.62 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 18 TYR 0.016 0.001 TYR J 49 PHE 0.027 0.002 PHE E 94 TRP 0.011 0.001 TRP I 47 HIS 0.001 0.000 HIS F 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (11974) covalent geometry : angle 0.58966 / 0.33 (16396) SS BOND : bond 0.00586 / 0.38 ( 12) SS BOND : angle 0.96903 / 0.61 ( 24) hydrogen bonds : bond 0.03286 / 2.21 ( 425) hydrogen bonds : angle 4.79471 / 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 235 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.447 Fit side-chains REVERT: B 81 GLU cc_start: 0.7876 (pp20) cc_final: 0.7540 (pp20) REVERT: C 15 LYS cc_start: 0.8723 (mttt) cc_final: 0.8050 (mmtt) REVERT: C 78 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8104 (mm-30) REVERT: E 12 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7859 (m) REVERT: E 41 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8004 (p0) REVERT: E 77 ASN cc_start: 0.7751 (p0) cc_final: 0.7448 (p0) REVERT: D 95 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8633 (ttp) REVERT: I 85 MET cc_start: 0.5358 (OUTLIER) cc_final: 0.5067 (pmt) REVERT: J 33 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6972 (tt) REVERT: K 111 TYR cc_start: 0.7509 (m-80) cc_final: 0.6492 (t80) REVERT: M 3 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: N 11 LEU cc_start: 0.4968 (OUTLIER) cc_final: 0.4587 (tm) outliers start: 52 outliers final: 37 residues processed: 219 average time/residue: 0.4808 time to fit residues: 115.4291 Evaluate side-chains 227 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 C residue 64 ASP 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 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 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 3 GLN 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 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 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: 1.9990 chunk 15 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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** N 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.155204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.121419 restraints weight = 14162.123| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.48 r_work: 0.3208 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 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 = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2395 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= 0.132 Angle : 0.581 8.457 16420 Z= 0.329 Chirality : 0.047 0.354 1772 Planarity : 0.004 0.039 1920 Dihedral : 16.215 147.342 1988 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 4.81 % Allowed : 28.95 % 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: -0.01 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.59 (0.20), residues: 654 loop : -0.57 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 18 TYR 0.016 0.001 TYR J 49 PHE 0.026 0.002 PHE F 94 TRP 0.014 0.001 TRP I 47 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (11974) covalent geometry : angle 0.58004 / 0.33 (16396) SS BOND : bond 0.00546 / 0.36 ( 12) SS BOND : angle 0.89179 / 0.56 ( 24) hydrogen bonds : bond 0.03149 / 2.12 ( 425) hydrogen bonds : angle 4.71935 / 3.28 ( 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 240 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.305 Fit side-chains REVERT: A 78 GLU cc_start: 0.8633 (tt0) cc_final: 0.8429 (mm-30) REVERT: B 81 GLU cc_start: 0.7894 (pp20) cc_final: 0.7528 (pp20) REVERT: C 15 LYS cc_start: 0.8709 (mttt) cc_final: 0.8025 (mmtt) REVERT: C 78 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8071 (mm-30) REVERT: E 12 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.7915 (m) REVERT: E 41 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7959 (p0) REVERT: E 77 ASN cc_start: 0.7716 (p0) cc_final: 0.7425 (p0) REVERT: D 95 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8627 (ttp) REVERT: I 85 MET cc_start: 0.5339 (OUTLIER) cc_final: 0.5115 (pmt) REVERT: J 33 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.6980 (tt) REVERT: K 111 TYR cc_start: 0.7491 (m-80) cc_final: 0.6455 (t80) REVERT: M 3 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: N 11 LEU cc_start: 0.4896 (OUTLIER) cc_final: 0.4519 (tm) outliers start: 56 outliers final: 41 residues processed: 224 average time/residue: 0.4647 time to fit residues: 114.1473 Evaluate side-chains 227 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 7 SER 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 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 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 3 GLN 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=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: 4.9990 chunk 102 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 0.0370 chunk 56 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- 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** N 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.154001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.120866 restraints weight = 14294.242| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.21 r_work: 0.3191 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- 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 = 0.00 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 = 0.00 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: 0.8730 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 : 0.004 0.037 11986 Z= 0.171 Angle : 0.622 9.949 16420 Z= 0.348 Chirality : 0.048 0.398 1772 Planarity : 0.004 0.039 1920 Dihedral : 16.185 147.306 1988 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 4.64 % Allowed : 29.30 % 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: -0.02 (0.22), residues: 1338 helix: None (None), residues: 0 sheet: 0.60 (0.21), residues: 654 loop : -0.59 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.016 0.002 TYR L 97 PHE 0.033 0.002 PHE F 94 TRP 0.015 0.001 TRP I 47 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (11974) covalent geometry : angle 0.62124 / 0.35 (16396) SS BOND : bond 0.00654 / 0.43 ( 12) SS BOND : angle 1.15301 / 0.72 ( 24) hydrogen bonds : bond 0.03445 / 2.31 ( 425) hydrogen bonds : angle 4.71298 / 3.28 ( 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 235 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 181 time to evaluate : 0.332 Fit side-chains REVERT: A 78 GLU cc_start: 0.8656 (tt0) cc_final: 0.8447 (mm-30) REVERT: B 81 GLU cc_start: 0.7859 (pp20) cc_final: 0.7526 (pp20) REVERT: C 15 LYS cc_start: 0.8700 (mttt) cc_final: 0.8029 (mmtt) REVERT: E 12 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.7911 (m) REVERT: E 41 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8002 (p0) REVERT: E 77 ASN cc_start: 0.7744 (p0) cc_final: 0.7449 (p0) REVERT: D 95 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8575 (tpp) REVERT: I 66 MET cc_start: 0.5082 (mpp) cc_final: 0.4867 (mtt) REVERT: I 85 MET cc_start: 0.5314 (OUTLIER) cc_final: 0.5112 (pmt) REVERT: J 33 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6994 (tt) REVERT: K 111 TYR cc_start: 0.7525 (m-80) cc_final: 0.6517 (t80) REVERT: M 3 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8135 (mt0) outliers start: 54 outliers final: 43 residues processed: 220 average time/residue: 0.4532 time to fit residues: 109.3379 Evaluate side-chains 230 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 64 ASP 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 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 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 3 GLN 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 95 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN M 34 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.153197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119646 restraints weight = 14306.003| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.29 r_work: 0.3183 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 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: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11986 Z= 0.211 Angle : 0.657 9.157 16420 Z= 0.367 Chirality : 0.050 0.431 1772 Planarity : 0.004 0.039 1920 Dihedral : 16.205 146.655 1986 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 4.73 % Allowed : 28.95 % Favored : 66.32 % 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 : -0.61 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 18 TYR 0.019 0.002 TYR L 97 PHE 0.037 0.002 PHE F 94 TRP 0.020 0.001 TRP I 47 HIS 0.002 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (11974) covalent geometry : angle 0.65528 / 0.37 (16396) SS BOND : bond 0.00712 / 0.47 ( 12) SS BOND : angle 1.31409 / 0.81 ( 24) hydrogen bonds : bond 0.03757 / 2.52 ( 425) hydrogen bonds : angle 4.74183 / 3.31 ( 1077) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4510.59 seconds wall clock time: 77 minutes 23.93 seconds (4643.93 seconds total)