Starting phenix.real_space_refine on Wed Aug 5 22:58:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tgn_55905/08_2026/9tgn_55905.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tgn_55905/08_2026/9tgn_55905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tgn_55905/08_2026/9tgn_55905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tgn_55905/08_2026/9tgn_55905.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tgn_55905/08_2026/9tgn_55905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tgn_55905/08_2026/9tgn_55905.map" } resolution = 2.55 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 47 5.49 5 Mg 8 5.21 5 S 60 5.16 5 C 7326 2.51 5 N 2034 2.21 5 O 2465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11940 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 105} Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 972 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 105} Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 972 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "E" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 105} Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 972 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "G" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 105} Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 972 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "I" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 105} Chain: "J" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 972 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "K" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 105} Chain: "L" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 972 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 244 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Conformer: "B" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} bond proxies already assigned to first conformer: 270 Chain: "N" 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: "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: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" 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: "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: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" 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} Time building chain proxies: 2.77, per 1000 atoms: 0.23 Number of scatterers: 11940 At special positions: 0 Unit cell: (146.858, 99.924, 105.98, 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 60 16.00 P 47 15.00 Mg 8 11.99 O 2465 8.00 N 2034 7.00 C 7326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 98 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 98 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 98 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 98 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 98 " distance=2.04 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: 0.92 Conformation dependent library (CDL) restraints added in 488.1 milliseconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 35 sheets defined 6.8% alpha, 48.3% beta 24 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.505A pdb=" N ASP A 82 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 83 " --> pdb=" O GLN A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 83' Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.559A pdb=" N THR B 93 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.585A pdb=" N ASP C 82 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 83 " --> pdb=" O GLN C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 83' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.547A pdb=" N THR D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.702A pdb=" N THR D 93 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.557A pdb=" N ASP E 82 " --> pdb=" O GLU E 79 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 83 " --> pdb=" O GLN E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 89 through 93 removed outlier: 4.007A pdb=" N THR F 93 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.911A pdb=" N ILE G 83 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.503A pdb=" N THR H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.655A pdb=" N ASP I 82 " --> pdb=" O GLU I 79 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE I 83 " --> pdb=" O GLN I 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 79 through 83' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.564A pdb=" N THR J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 53 through 57 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.616A pdb=" N ILE K 83 " --> pdb=" O GLN K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.685A pdb=" N ASN L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 57 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.516A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 3.639A pdb=" N ILE A 48 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN A 37 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU A 46 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 13 removed outlier: 3.971A pdb=" N THR A 97 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.089A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.629A pdb=" N TYR B 111 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.278A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.896A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.789A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.541A pdb=" N TYR D 111 " --> pdb=" O ARG D 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.830A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.950A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.170A pdb=" N GLY F 10 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N MET F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.170A pdb=" N GLY F 10 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR F 111 " --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AC2, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 54 removed outlier: 5.568A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE G 48 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.085A pdb=" N GLY H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.085A pdb=" N GLY H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR H 111 " --> pdb=" O ARG H 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.604A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.554A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.474A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.474A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR J 111 " --> pdb=" O ARG J 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.595A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.988A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 3 through 7 removed outlier: 5.750A pdb=" N GLY L 16 " --> pdb=" O ASN L 87 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.954A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.463A pdb=" N ARG L 100 " --> pdb=" O ASP L 110 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2075 1.32 - 1.45: 3760 1.45 - 1.57: 6227 1.57 - 1.70: 93 1.70 - 1.82: 96 Bond restraints: 12251 Sorted by residual: bond pdb=" CG PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 1.503 1.200 0.303 3.40e-02 8.65e+02 7.94e+01 bond pdb=" C3' DG M 2 " pdb=" C2' DG M 2 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.64e+00 bond pdb=" N PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 1.473 1.514 -0.041 1.40e-02 5.10e+03 8.53e+00 bond pdb=" O4' DC M 9 " pdb=" C1' DC M 9 " ideal model delta sigma weight residual 1.420 1.388 0.032 1.10e-02 8.26e+03 8.43e+00 bond pdb=" C3' DC N 1 " pdb=" C2' DC N 1 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.18e+00 ... (remaining 12246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 16762 4.68 - 9.36: 27 9.36 - 14.04: 1 14.04 - 18.72: 0 18.72 - 23.40: 2 Bond angle restraints: 16792 Sorted by residual: angle pdb=" N PRO D 41 " pdb=" CD PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 103.20 82.34 20.86 1.50e+00 4.44e-01 1.93e+02 angle pdb=" CA PRO D 41 " pdb=" CB PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 104.50 81.10 23.40 1.90e+00 2.77e-01 1.52e+02 angle pdb=" N PRO D 41 " pdb=" CA PRO D 41 " pdb=" CB PRO D 41 " ideal model delta sigma weight residual 103.17 96.90 6.27 8.90e-01 1.26e+00 4.96e+01 angle pdb=" CA PRO D 41 " pdb=" N PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 112.00 104.98 7.02 1.40e+00 5.10e-01 2.52e+01 angle pdb=" C TYR A 50 " pdb=" N THR A 51 " pdb=" CA THR A 51 " ideal model delta sigma weight residual 121.54 131.00 -9.46 1.91e+00 2.74e-01 2.45e+01 ... (remaining 16787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.39: 6512 32.39 - 64.78: 535 64.78 - 97.18: 21 97.18 - 129.57: 4 129.57 - 161.96: 1 Dihedral angle restraints: 7073 sinusoidal: 3035 harmonic: 4038 Sorted by residual: dihedral pdb=" C4' DC N 1 " pdb=" C3' DC N 1 " pdb=" O3' DC N 1 " pdb=" P DG N 2 " ideal model delta sinusoidal sigma weight residual 220.00 58.04 161.96 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA TYR F 102 " pdb=" C TYR F 102 " pdb=" N VAL F 103 " pdb=" CA VAL F 103 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" N PRO D 41 " pdb=" CG PRO D 41 " pdb=" CD PRO D 41 " pdb=" CB PRO D 41 " ideal model delta sinusoidal sigma weight residual 30.00 76.98 -46.98 1 1.50e+01 4.44e-03 1.36e+01 ... (remaining 7070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1171 0.037 - 0.075: 433 0.075 - 0.112: 182 0.112 - 0.149: 50 0.149 - 0.186: 8 Chirality restraints: 1844 Sorted by residual: chirality pdb=" C3' DC N 1 " pdb=" C4' DC N 1 " pdb=" O3' DC N 1 " pdb=" C2' DC N 1 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CA THR A 51 " pdb=" N THR A 51 " pdb=" C THR A 51 " pdb=" CB THR A 51 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" C3' DG O 8 " pdb=" C4' DG O 8 " pdb=" O3' DG O 8 " pdb=" C2' DG O 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 1841 not shown) Planarity restraints: 1968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU K 81 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C GLU K 81 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU K 81 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP K 82 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 51 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C THR C 51 " 0.034 2.00e-02 2.50e+03 pdb=" O THR C 51 " -0.012 2.00e-02 2.50e+03 pdb=" N SER C 52 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 51 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C THR E 51 " 0.030 2.00e-02 2.50e+03 pdb=" O THR E 51 " -0.011 2.00e-02 2.50e+03 pdb=" N SER E 52 " -0.010 2.00e-02 2.50e+03 ... (remaining 1965 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 767 2.73 - 3.28: 9951 3.28 - 3.82: 18593 3.82 - 4.36: 24908 4.36 - 4.90: 42590 Nonbonded interactions: 96809 Sorted by model distance: nonbonded pdb=" OG SER I 14 " pdb=" OD1 ASP I 17 " model vdw 2.192 3.040 nonbonded pdb=" N GLU J 91 " pdb=" OE1 GLU J 91 " model vdw 2.269 3.120 nonbonded pdb=" NH1 ARG I 61 " pdb=" OD2 ASP I 82 " model vdw 2.276 3.120 nonbonded pdb=" NH1 ARG K 61 " pdb=" OD2 ASP K 82 " model vdw 2.304 3.120 nonbonded pdb=" O THR C 8 " pdb=" OG1 THR C 102 " model vdw 2.318 3.040 ... (remaining 96804 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 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = (chain 'M' and (resid 1 or resid 3 through 5 or resid 7 through 101)) selection = (chain 'N' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name C1' or name N1 or name C2 or name O2 or n \ ame N3 or name C4 or name N4 or name C5 or name C6 )) or resid 3 through 5 or re \ sid 7 through 101)) selection = (chain 'O' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name C1' or name N1 or name C2 or name O2 or n \ ame N3 or name C4 or name N4 or name C5 or name C6 )) or resid 3 through 5 or re \ sid 7 through 101)) selection = (chain 'P' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name C1' or name N1 or name C2 or name O2 or n \ ame N3 or name C4 or name N4 or name C5 or name C6 )) or resid 3 through 5 or re \ sid 7 through 101)) } 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=0.37 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: 12.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.950 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:9.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 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 : 0.006 0.303 12263 Z= 0.347 Angle : 0.716 23.402 16816 Z= 0.461 Chirality : 0.048 0.186 1844 Planarity : 0.004 0.034 1968 Dihedral : 20.085 161.959 4481 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.28 % Allowed : 26.55 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.34 (0.22), residues: 1368 helix: None (None), residues: 0 sheet: 0.08 (0.19), residues: 690 loop : -0.45 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 24 TYR 0.011 0.002 TYR B 111 PHE 0.013 0.002 PHE K 87 TRP 0.009 0.001 TRP L 47 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.35 (12251) covalent geometry : angle 0.71335 / 0.46 (16792) SS BOND : bond 0.00828 / 0.53 ( 12) SS BOND : angle 1.77238 / 1.13 ( 24) hydrogen bonds : bond 0.11606 / 8.01 ( 472) hydrogen bonds : angle 5.71097 / 3.87 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 0.379 Fit side-chains outliers start: 63 outliers final: 59 residues processed: 243 average time/residue: 0.5403 time to fit residues: 143.3080 Evaluate side-chains 243 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 41 PRO Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099087 restraints weight = 12555.972| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.95 r_work: 0.3206 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.0393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12263 Z= 0.278 Angle : 0.747 10.886 16816 Z= 0.409 Chirality : 0.051 0.370 1844 Planarity : 0.004 0.036 1968 Dihedral : 17.377 162.413 2111 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 8.46 % Allowed : 22.86 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.41 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.10 (0.19), residues: 678 loop : -0.57 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 24 TYR 0.014 0.003 TYR B 111 PHE 0.016 0.003 PHE K 87 TRP 0.009 0.002 TRP H 112 HIS 0.002 0.001 HIS K 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.28 (12251) covalent geometry : angle 0.74290 / 0.41 (16792) SS BOND : bond 0.00996 / 0.65 ( 12) SS BOND : angle 2.10076 / 1.34 ( 24) hydrogen bonds : bond 0.05063 / 3.51 ( 472) hydrogen bonds : angle 4.90759 / 3.34 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 187 time to evaluate : 0.471 Fit side-chains REVERT: A 18 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6688 (ttm170) REVERT: D 46 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8630 (tt0) REVERT: D 89 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7394 (mttm) REVERT: E 104 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7836 (mp) REVERT: F 110 ASP cc_start: 0.8571 (p0) cc_final: 0.8347 (p0) REVERT: G 94 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8271 (mp) REVERT: I 24 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7022 (ttp80) REVERT: J 18 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7043 (tt) REVERT: K 73 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.6943 (tp) REVERT: K 103 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7082 (tptm) REVERT: L 85 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8182 (mtp) outliers start: 101 outliers final: 58 residues processed: 264 average time/residue: 0.5129 time to fit residues: 148.1486 Evaluate side-chains 253 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 185 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 110 ASP Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 121 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 93 optimal weight: 0.0670 chunk 105 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102966 restraints weight = 12550.959| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.96 r_work: 0.3248 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12263 Z= 0.115 Angle : 0.554 8.262 16816 Z= 0.317 Chirality : 0.043 0.293 1844 Planarity : 0.003 0.033 1968 Dihedral : 16.943 161.329 2080 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.03 % Allowed : 25.46 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.23 (0.22), residues: 1368 helix: None (None), residues: 0 sheet: 0.20 (0.19), residues: 690 loop : -0.44 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 24 TYR 0.009 0.001 TYR K 77 PHE 0.016 0.001 PHE B 29 TRP 0.009 0.001 TRP H 47 HIS 0.000 0.000 HIS C 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.12 (12251) covalent geometry : angle 0.55286 / 0.32 (16792) SS BOND : bond 0.00564 / 0.36 ( 12) SS BOND : angle 1.03540 / 0.65 ( 24) hydrogen bonds : bond 0.03209 / 2.11 ( 472) hydrogen bonds : angle 4.61180 / 3.15 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 0.530 Fit side-chains REVERT: D 95 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8575 (tpp) REVERT: F 110 ASP cc_start: 0.8510 (p0) cc_final: 0.8303 (p0) REVERT: G 94 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8233 (mp) REVERT: I 24 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6752 (ttp80) REVERT: I 107 LYS cc_start: 0.7594 (tttp) cc_final: 0.7174 (ttpt) REVERT: K 79 GLU cc_start: 0.5858 (OUTLIER) cc_final: 0.4176 (mp0) REVERT: L 85 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8192 (mtp) outliers start: 60 outliers final: 41 residues processed: 231 average time/residue: 0.5321 time to fit residues: 134.0006 Evaluate side-chains 233 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 1 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.135460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099136 restraints weight = 12547.624| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.95 r_work: 0.3198 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 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 (13 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.0540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12263 Z= 0.277 Angle : 0.744 11.006 16816 Z= 0.407 Chirality : 0.051 0.361 1844 Planarity : 0.004 0.036 1968 Dihedral : 16.997 163.068 2064 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 6.62 % Allowed : 24.04 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.13 (0.19), residues: 690 loop : -0.55 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 24 TYR 0.015 0.003 TYR A 32 PHE 0.016 0.003 PHE F 29 TRP 0.010 0.002 TRP H 112 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.28 (12251) covalent geometry : angle 0.74056 / 0.41 (16792) SS BOND : bond 0.00996 / 0.65 ( 12) SS BOND : angle 2.04248 / 1.31 ( 24) hydrogen bonds : bond 0.04993 / 3.48 ( 472) hydrogen bonds : angle 4.72175 / 3.20 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 190 time to evaluate : 0.423 Fit side-chains REVERT: A 103 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7986 (ttmt) REVERT: D 46 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8655 (tt0) REVERT: D 89 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7389 (mttm) REVERT: D 95 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8597 (tpp) REVERT: G 94 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8286 (mp) REVERT: H 100 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.7576 (ttm170) REVERT: I 24 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7019 (ttp80) REVERT: K 73 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.6965 (tp) REVERT: K 79 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.4483 (mp0) REVERT: K 103 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.6965 (tptm) REVERT: L 46 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: L 85 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8198 (mtp) REVERT: L 91 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.6078 (pm20) outliers start: 79 outliers final: 46 residues processed: 242 average time/residue: 0.4971 time to fit residues: 130.9826 Evaluate side-chains 246 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102275 restraints weight = 12572.854| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.94 r_work: 0.3238 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 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 = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12263 Z= 0.132 Angle : 0.586 9.460 16816 Z= 0.333 Chirality : 0.044 0.309 1844 Planarity : 0.004 0.033 1968 Dihedral : 16.818 162.022 2062 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 6.62 % Allowed : 24.20 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.31 (0.22), residues: 1368 helix: None (None), residues: 0 sheet: 0.05 (0.18), residues: 726 loop : -0.38 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 24 TYR 0.009 0.001 TYR H 97 PHE 0.015 0.002 PHE B 29 TRP 0.010 0.001 TRP H 47 HIS 0.000 0.000 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (12251) covalent geometry : angle 0.58494 / 0.33 (16792) SS BOND : bond 0.00668 / 0.43 ( 12) SS BOND : angle 1.21782 / 0.78 ( 24) hydrogen bonds : bond 0.03425 / 2.27 ( 472) hydrogen bonds : angle 4.51445 / 3.08 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 186 time to evaluate : 0.331 Fit side-chains REVERT: A 103 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7859 (ttmt) REVERT: C 103 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8192 (tttt) REVERT: D 46 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: D 95 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8553 (tpp) REVERT: G 94 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8226 (mp) REVERT: H 100 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.7432 (ttm170) REVERT: I 24 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6800 (ttp80) REVERT: J 80 MET cc_start: 0.8108 (mmm) cc_final: 0.7833 (mmm) REVERT: K 73 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.6828 (tp) REVERT: K 79 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.4214 (mp0) REVERT: L 85 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8210 (mtp) REVERT: L 91 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.6079 (pm20) outliers start: 79 outliers final: 45 residues processed: 241 average time/residue: 0.5126 time to fit residues: 136.8041 Evaluate side-chains 240 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 102 optimal weight: 0.0270 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.100372 restraints weight = 12553.914| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.94 r_work: 0.3215 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 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 = 0.3101 r_free = 0.3101 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 (7 function evaluations) r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12263 Z= 0.214 Angle : 0.678 9.780 16816 Z= 0.375 Chirality : 0.048 0.343 1844 Planarity : 0.004 0.035 1968 Dihedral : 16.792 163.135 2059 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 6.87 % Allowed : 24.04 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.01 (0.18), residues: 726 loop : -0.42 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 24 TYR 0.013 0.002 TYR F 111 PHE 0.014 0.002 PHE I 98 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (12251) covalent geometry : angle 0.67503 / 0.37 (16792) SS BOND : bond 0.00877 / 0.56 ( 12) SS BOND : angle 1.71330 / 1.10 ( 24) hydrogen bonds : bond 0.04321 / 2.97 ( 472) hydrogen bonds : angle 4.54114 / 3.10 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 188 time to evaluate : 0.476 Fit side-chains REVERT: A 18 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6672 (ttm170) REVERT: A 103 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7924 (ttmt) REVERT: D 46 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8640 (tt0) REVERT: D 89 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7360 (mttm) REVERT: D 95 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8585 (tpp) REVERT: G 33 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8524 (tm) REVERT: G 94 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8271 (mp) REVERT: H 57 ASN cc_start: 0.8245 (m110) cc_final: 0.7945 (m-40) REVERT: H 100 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.7434 (ttm170) REVERT: I 24 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6907 (ttp80) REVERT: J 80 MET cc_start: 0.8167 (mmm) cc_final: 0.7883 (mmm) REVERT: K 73 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.6887 (tp) REVERT: K 79 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.4391 (mp0) REVERT: L 85 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8181 (mtp) REVERT: L 91 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6098 (pm20) outliers start: 82 outliers final: 56 residues processed: 245 average time/residue: 0.5092 time to fit residues: 135.9092 Evaluate side-chains 256 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 187 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 0.4980 chunk 122 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.102957 restraints weight = 12517.156| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.94 r_work: 0.3248 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12263 Z= 0.122 Angle : 0.564 9.281 16816 Z= 0.322 Chirality : 0.043 0.301 1844 Planarity : 0.003 0.034 1968 Dihedral : 16.621 163.088 2056 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.44 % Allowed : 25.63 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.25 (0.22), residues: 1368 helix: None (None), residues: 0 sheet: 0.09 (0.18), residues: 726 loop : -0.35 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 24 TYR 0.009 0.001 TYR F 111 PHE 0.014 0.001 PHE B 29 TRP 0.011 0.001 TRP H 47 HIS 0.000 0.000 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (12251) covalent geometry : angle 0.56311 / 0.32 (16792) SS BOND : bond 0.00587 / 0.37 ( 12) SS BOND : angle 1.05904 / 0.68 ( 24) hydrogen bonds : bond 0.03160 / 2.08 ( 472) hydrogen bonds : angle 4.40674 / 3.02 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 0.457 Fit side-chains REVERT: A 103 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7883 (ttmt) REVERT: D 89 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7290 (mttm) REVERT: D 95 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8573 (tpp) REVERT: E 33 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7988 (tm) REVERT: G 33 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8404 (tm) REVERT: G 94 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8229 (mp) REVERT: H 57 ASN cc_start: 0.8197 (m110) cc_final: 0.7898 (m-40) REVERT: H 100 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7248 (ttm170) REVERT: I 24 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6771 (ttp80) REVERT: J 80 MET cc_start: 0.8126 (mmm) cc_final: 0.7817 (mmm) REVERT: K 73 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6810 (tp) REVERT: K 79 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.4200 (mp0) REVERT: L 85 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8189 (mtp) REVERT: L 91 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.6109 (pm20) outliers start: 65 outliers final: 39 residues processed: 235 average time/residue: 0.5050 time to fit residues: 129.3840 Evaluate side-chains 234 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 38 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 12 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 GLN G 55 HIS H 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.134831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098369 restraints weight = 12517.112| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.96 r_work: 0.3195 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 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 = 0.3081 r_free = 0.3081 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 (5 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 12263 Z= 0.324 Angle : 0.797 11.883 16816 Z= 0.432 Chirality : 0.054 0.374 1844 Planarity : 0.005 0.043 1968 Dihedral : 16.763 163.511 2052 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.11 % Allowed : 25.46 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.45 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: -0.04 (0.18), residues: 726 loop : -0.48 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 24 TYR 0.018 0.003 TYR F 111 PHE 0.017 0.003 PHE K 87 TRP 0.010 0.002 TRP H 112 HIS 0.001 0.000 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.32 (12251) covalent geometry : angle 0.79301 / 0.43 (16792) SS BOND : bond 0.01086 / 0.70 ( 12) SS BOND : angle 2.27367 / 1.47 ( 24) hydrogen bonds : bond 0.05386 / 3.78 ( 472) hydrogen bonds : angle 4.66324 / 3.19 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 183 time to evaluate : 0.317 Fit side-chains REVERT: A 103 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7972 (ttmt) REVERT: D 46 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8655 (tt0) REVERT: D 89 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7389 (mttm) REVERT: G 94 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8293 (mp) REVERT: H 57 ASN cc_start: 0.8282 (m110) cc_final: 0.7983 (m-40) REVERT: H 100 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.7398 (ttm170) REVERT: I 24 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7056 (ttp80) REVERT: K 73 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.6969 (tp) REVERT: K 79 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.4604 (mp0) REVERT: L 85 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8208 (mtp) REVERT: L 91 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.6080 (pm20) outliers start: 73 outliers final: 46 residues processed: 234 average time/residue: 0.4788 time to fit residues: 121.3620 Evaluate side-chains 240 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 117 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102915 restraints weight = 12464.274| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.94 r_work: 0.3250 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12263 Z= 0.125 Angle : 0.574 10.218 16816 Z= 0.327 Chirality : 0.044 0.308 1844 Planarity : 0.003 0.034 1968 Dihedral : 16.568 162.288 2051 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.94 % Allowed : 27.64 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.30 (0.22), residues: 1368 helix: None (None), residues: 0 sheet: 0.06 (0.18), residues: 726 loop : -0.38 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 24 TYR 0.010 0.001 TYR H 97 PHE 0.015 0.001 PHE B 29 TRP 0.013 0.001 TRP H 47 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (12251) covalent geometry : angle 0.57262 / 0.33 (16792) SS BOND : bond 0.00597 / 0.38 ( 12) SS BOND : angle 1.12588 / 0.72 ( 24) hydrogen bonds : bond 0.03166 / 2.07 ( 472) hydrogen bonds : angle 4.45262 / 3.05 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.441 Fit side-chains REVERT: A 103 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7877 (ttmt) REVERT: C 103 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8144 (tttt) REVERT: D 89 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7334 (mttm) REVERT: G 94 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8236 (mp) REVERT: H 57 ASN cc_start: 0.8177 (m110) cc_final: 0.7877 (m-40) REVERT: H 100 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.7207 (ttm170) REVERT: I 24 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6717 (ttp80) REVERT: K 73 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.6785 (tp) REVERT: K 79 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.4174 (mp0) REVERT: L 85 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8192 (mtp) REVERT: L 91 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.6109 (pm20) outliers start: 47 outliers final: 31 residues processed: 220 average time/residue: 0.5413 time to fit residues: 129.4753 Evaluate side-chains 223 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 129 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 75 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.137555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101389 restraints weight = 12527.342| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.96 r_work: 0.3225 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 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 = 0.3109 r_free = 0.3109 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 (5 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12263 Z= 0.167 Angle : 0.630 10.238 16816 Z= 0.352 Chirality : 0.046 0.321 1844 Planarity : 0.004 0.037 1968 Dihedral : 16.506 164.442 2050 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.19 % Allowed : 27.72 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.31 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.05 (0.18), residues: 726 loop : -0.39 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 24 TYR 0.011 0.002 TYR F 111 PHE 0.013 0.002 PHE B 29 TRP 0.010 0.001 TRP H 47 HIS 0.000 0.000 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (12251) covalent geometry : angle 0.62790 / 0.35 (16792) SS BOND : bond 0.00775 / 0.50 ( 12) SS BOND : angle 1.54445 / 1.00 ( 24) hydrogen bonds : bond 0.03730 / 2.53 ( 472) hydrogen bonds : angle 4.43013 / 3.03 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 0.287 Fit side-chains REVERT: A 11 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7318 (tt) REVERT: A 103 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7877 (ttmt) REVERT: D 89 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7278 (mttm) REVERT: G 94 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8222 (mp) REVERT: H 57 ASN cc_start: 0.8216 (m110) cc_final: 0.7912 (m-40) REVERT: H 100 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.7189 (ttm170) REVERT: I 24 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6759 (ttp80) REVERT: K 73 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.6863 (tp) REVERT: K 79 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.4267 (mp0) REVERT: L 85 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8180 (mtp) REVERT: L 91 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6114 (pm20) outliers start: 50 outliers final: 34 residues processed: 218 average time/residue: 0.5541 time to fit residues: 131.0334 Evaluate side-chains 228 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 135 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101043 restraints weight = 12453.421| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.96 r_work: 0.3230 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 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 = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12263 Z= 0.167 Angle : 0.633 10.205 16816 Z= 0.352 Chirality : 0.046 0.321 1844 Planarity : 0.004 0.035 1968 Dihedral : 16.509 164.527 2050 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.52 % Allowed : 27.72 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.31 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.05 (0.18), residues: 726 loop : -0.39 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 24 TYR 0.010 0.002 TYR H 111 PHE 0.012 0.002 PHE C 98 TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (12251) covalent geometry : angle 0.63030 / 0.35 (16792) SS BOND : bond 0.00762 / 0.49 ( 12) SS BOND : angle 1.59298 / 1.03 ( 24) hydrogen bonds : bond 0.03693 / 2.50 ( 472) hydrogen bonds : angle 4.43118 / 3.03 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5314.90 seconds wall clock time: 90 minutes 52.37 seconds (5452.37 seconds total)