Starting phenix.real_space_refine on Thu Feb 5 10:23:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4f_48874/02_2026/9n4f_48874.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4f_48874/02_2026/9n4f_48874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n4f_48874/02_2026/9n4f_48874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4f_48874/02_2026/9n4f_48874.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n4f_48874/02_2026/9n4f_48874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4f_48874/02_2026/9n4f_48874.map" } resolution = 2.71 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= 0.001 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 10278 2.51 5 N 2877 2.21 5 O 3246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16473 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2410 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 19, 'TRANS': 292} Chain breaks: 1 Chain: "B" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'TRANS': 163} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 941 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 795 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "C" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2410 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 19, 'TRANS': 292} Chain breaks: 1 Chain: "D" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'TRANS': 163} Chain: "M" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 941 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "N" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 795 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "E" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2410 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 19, 'TRANS': 292} Chain breaks: 1 Chain: "F" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1345 Classifications: {'peptide': 164} Link IDs: {'TRANS': 163} Chain: "O" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 941 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "P" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 795 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Time building chain proxies: 3.81, per 1000 atoms: 0.23 Number of scatterers: 16473 At special positions: 0 Unit cell: (119.025, 118.496, 144.946, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3246 8.00 N 2877 7.00 C 10278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=0.98 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=1.24 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=1.24 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 730.2 milliseconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 57 sheets defined 19.9% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.074A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 38 through 57 Processing helix chain 'B' and resid 75 through 126 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.067A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 4.074A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 38 through 57 Processing helix chain 'D' and resid 75 through 126 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'M' and resid 83 through 87 removed outlier: 4.066A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 4.074A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 38 through 57 Processing helix chain 'F' and resid 75 through 126 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'O' and resid 83 through 87 removed outlier: 4.067A pdb=" N THR O 87 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.029A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.658A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.125A pdb=" N VAL A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY A 256 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.662A pdb=" N CYS A 139 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 removed outlier: 5.451A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288 removed outlier: 3.764A pdb=" N ILE A 288 " --> pdb=" O CYS A 281 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 22 through 27 removed outlier: 4.595A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.580A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.745A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.795A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AC2, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC3, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.029A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.659A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.125A pdb=" N VAL C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY C 256 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC9, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.662A pdb=" N CYS C 139 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 169 removed outlier: 5.452A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.764A pdb=" N ILE C 288 " --> pdb=" O CYS C 281 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 22 through 27 removed outlier: 4.595A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AD6, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.580A pdb=" N THR M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.744A pdb=" N MET M 34 " --> pdb=" O THR M 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AD9, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.795A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 9 through 13 Processing sheet with id=AE2, first strand: chain 'N' and resid 18 through 24 Processing sheet with id=AE3, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AE4, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AE5, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AE6, first strand: chain 'E' and resid 51 through 52 removed outlier: 6.030A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.658A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 100 through 101 removed outlier: 5.125A pdb=" N VAL E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY E 256 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AF1, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.662A pdb=" N CYS E 139 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AF3, first strand: chain 'E' and resid 164 through 169 removed outlier: 5.452A pdb=" N ARG E 201 " --> pdb=" O ASN E 248 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 286 through 288 removed outlier: 3.765A pdb=" N ILE E 288 " --> pdb=" O CYS E 281 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 22 through 27 removed outlier: 4.594A pdb=" N TYR F 22 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 130 through 132 Processing sheet with id=AF7, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.581A pdb=" N THR O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.745A pdb=" N MET O 34 " --> pdb=" O THR O 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 11 through 12 Processing sheet with id=AG1, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.795A pdb=" N TRP P 35 " --> pdb=" O ILE P 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 9 through 13 Processing sheet with id=AG3, first strand: chain 'P' and resid 18 through 24 702 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5499 1.34 - 1.46: 4071 1.46 - 1.58: 7164 1.58 - 1.70: 0 1.70 - 1.82: 99 Bond restraints: 16833 Sorted by residual: bond pdb=" N ASP L 50 " pdb=" CA ASP L 50 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.45e+00 bond pdb=" N TYR L 49 " pdb=" CA TYR L 49 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.15e-02 7.56e+03 9.22e+00 bond pdb=" N ARG A 62 " pdb=" CA ARG A 62 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.23e-02 6.61e+03 7.10e+00 bond pdb=" N LEU F 110 " pdb=" CA LEU F 110 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.33e-02 5.65e+03 7.04e+00 bond pdb=" N ASP D 109 " pdb=" CA ASP D 109 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.85e+00 ... (remaining 16828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 22261 1.86 - 3.72: 446 3.72 - 5.58: 94 5.58 - 7.45: 14 7.45 - 9.31: 6 Bond angle restraints: 22821 Sorted by residual: angle pdb=" CB GLU D 131 " pdb=" CG GLU D 131 " pdb=" CD GLU D 131 " ideal model delta sigma weight residual 112.60 103.29 9.31 1.70e+00 3.46e-01 3.00e+01 angle pdb=" CA TRP M 100 " pdb=" C TRP M 100 " pdb=" O TRP M 100 " ideal model delta sigma weight residual 121.84 115.87 5.97 1.16e+00 7.43e-01 2.64e+01 angle pdb=" CA PHE A 258 " pdb=" CB PHE A 258 " pdb=" CG PHE A 258 " ideal model delta sigma weight residual 113.80 118.89 -5.09 1.00e+00 1.00e+00 2.59e+01 angle pdb=" N VAL M 63 " pdb=" CA VAL M 63 " pdb=" C VAL M 63 " ideal model delta sigma weight residual 113.71 108.96 4.75 9.50e-01 1.11e+00 2.50e+01 angle pdb=" N VAL H 63 " pdb=" CA VAL H 63 " pdb=" C VAL H 63 " ideal model delta sigma weight residual 113.71 108.97 4.74 9.50e-01 1.11e+00 2.49e+01 ... (remaining 22816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8473 17.92 - 35.83: 1081 35.83 - 53.75: 323 53.75 - 71.66: 71 71.66 - 89.58: 27 Dihedral angle restraints: 9975 sinusoidal: 3936 harmonic: 6039 Sorted by residual: dihedral pdb=" CB CYS E 52 " pdb=" SG CYS E 52 " pdb=" SG CYS E 277 " pdb=" CB CYS E 277 " ideal model delta sinusoidal sigma weight residual -86.00 -175.58 89.58 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -175.12 89.12 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CD ARG E 261 " pdb=" NE ARG E 261 " pdb=" CZ ARG E 261 " pdb=" NH1 ARG E 261 " ideal model delta sinusoidal sigma weight residual 0.00 82.21 -82.21 1 1.00e+01 1.00e-02 8.30e+01 ... (remaining 9972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2200 0.070 - 0.139: 249 0.139 - 0.209: 8 0.209 - 0.279: 2 0.279 - 0.349: 4 Chirality restraints: 2463 Sorted by residual: chirality pdb=" CA ARG E 261 " pdb=" N ARG E 261 " pdb=" C ARG E 261 " pdb=" CB ARG E 261 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA ARG C 261 " pdb=" N ARG C 261 " pdb=" C ARG C 261 " pdb=" CB ARG C 261 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA ARG A 261 " pdb=" N ARG A 261 " pdb=" C ARG A 261 " pdb=" CB ARG A 261 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 2460 not shown) Planarity restraints: 2985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 261 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 261 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 261 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 261 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 261 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 261 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG E 261 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 261 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG E 261 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG E 261 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 261 " 1.097 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG C 261 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 261 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 261 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 261 " 0.018 2.00e-02 2.50e+03 ... (remaining 2982 not shown) Histogram of nonbonded interaction distances: 0.49 - 1.37: 2 1.37 - 2.25: 9 2.25 - 3.14: 11937 3.14 - 4.02: 42166 4.02 - 4.90: 80471 Warning: very small nonbonded interaction distances. Nonbonded interactions: 134585 Sorted by model distance: nonbonded pdb=" CD ARG B 127 " pdb=" OE2 GLU F 131 " model vdw 0.491 3.440 nonbonded pdb=" NE ARG B 127 " pdb=" OE2 GLU F 131 " model vdw 1.308 3.120 nonbonded pdb=" CD ARG B 127 " pdb=" CD GLU F 131 " model vdw 1.579 3.670 nonbonded pdb=" CG ARG B 127 " pdb=" OE2 GLU F 131 " model vdw 1.921 3.440 nonbonded pdb=" CB VAL C 323 " pdb=" NH2 ARG P 27 " model vdw 1.930 3.550 ... (remaining 134580 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 32.980 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: 0.580 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.410 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.013 1.050 16852 Z= 0.708 Angle : 1.049 72.806 22857 Z= 0.552 Chirality : 0.046 0.349 2463 Planarity : 0.022 0.492 2985 Dihedral : 17.681 89.124 6081 Min Nonbonded Distance : 0.491 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.94 % Rotamer: Outliers : 3.61 % Allowed : 27.44 % Favored : 68.94 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2094 helix: 0.94 (0.26), residues: 360 sheet: 0.72 (0.21), residues: 567 loop : -1.30 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 57 TYR 0.010 0.001 TYR P 49 PHE 0.015 0.001 PHE D 9 TRP 0.013 0.001 TRP A 222 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00446 (16833) covalent geometry : angle 0.65915 (22821) SS BOND : bond 0.36204 ( 18) SS BOND : angle 20.57183 ( 36) hydrogen bonds : bond 0.22031 ( 672) hydrogen bonds : angle 7.68791 ( 1863) Misc. bond : bond 0.41596 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 406 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7962 (t0) cc_final: 0.7759 (t0) REVERT: A 295 GLN cc_start: 0.8568 (pp30) cc_final: 0.8336 (pm20) REVERT: C 34 ILE cc_start: 0.8659 (pt) cc_final: 0.8265 (mm) REVERT: C 50 LYS cc_start: 0.8371 (mttm) cc_final: 0.8166 (mttp) REVERT: C 126 THR cc_start: 0.8333 (m) cc_final: 0.8087 (t) REVERT: C 157 SER cc_start: 0.8010 (OUTLIER) cc_final: 0.7760 (p) REVERT: D 52 LEU cc_start: 0.8170 (tp) cc_final: 0.7937 (tp) REVERT: D 128 GLU cc_start: 0.5969 (mt-10) cc_final: 0.5596 (mt-10) REVERT: D 137 CYS cc_start: 0.8176 (p) cc_final: 0.7505 (m) REVERT: M 43 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7759 (mtmp) REVERT: N 27 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6998 (ttm110) REVERT: E 34 ILE cc_start: 0.8464 (pt) cc_final: 0.8109 (mm) REVERT: E 45 SER cc_start: 0.8484 (p) cc_final: 0.8167 (t) REVERT: E 156 LYS cc_start: 0.8525 (pttt) cc_final: 0.8213 (pttm) REVERT: E 157 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8163 (p) REVERT: E 168 MET cc_start: 0.8076 (tpp) cc_final: 0.7685 (tpp) REVERT: E 182 VAL cc_start: 0.8756 (t) cc_final: 0.8549 (p) REVERT: F 116 ASN cc_start: 0.7959 (t0) cc_final: 0.7705 (t0) REVERT: O 17 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7806 (m) outliers start: 65 outliers final: 26 residues processed: 458 average time/residue: 0.5489 time to fit residues: 282.3900 Evaluate side-chains 402 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 371 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 111 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 298 ASN B 125 GLN C 54 ASN D 116 ASN D 125 GLN E 44 GLN E 54 ASN E 137 ASN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN F 53 ASN F 95 ASN F 104 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN F 169 ASN P 38 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110377 restraints weight = 23268.470| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.70 r_work: 0.3359 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16852 Z= 0.248 Angle : 0.605 12.159 22857 Z= 0.323 Chirality : 0.045 0.154 2463 Planarity : 0.005 0.051 2985 Dihedral : 5.200 36.462 2343 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.78 % Allowed : 26.00 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2094 helix: 2.58 (0.25), residues: 360 sheet: 0.78 (0.21), residues: 573 loop : -1.36 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 123 TYR 0.017 0.002 TYR E 195 PHE 0.018 0.002 PHE B 24 TRP 0.024 0.002 TRP C 222 HIS 0.011 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00577 (16833) covalent geometry : angle 0.60000 (22821) SS BOND : bond 0.00790 ( 18) SS BOND : angle 2.02658 ( 36) hydrogen bonds : bond 0.05486 ( 672) hydrogen bonds : angle 5.19102 ( 1863) Misc. bond : bond 0.00327 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 348 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8665 (mm110) REVERT: B 30 GLU cc_start: 0.7837 (mp0) cc_final: 0.7507 (mp0) REVERT: B 97 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7615 (mt-10) REVERT: B 128 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6760 (mp0) REVERT: C 34 ILE cc_start: 0.8523 (pt) cc_final: 0.8201 (mm) REVERT: C 126 THR cc_start: 0.8467 (m) cc_final: 0.8222 (t) REVERT: D 72 GLU cc_start: 0.7475 (mp0) cc_final: 0.7001 (mp0) REVERT: M 43 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8117 (mtmp) REVERT: E 34 ILE cc_start: 0.8300 (pt) cc_final: 0.8086 (mm) REVERT: E 182 VAL cc_start: 0.8450 (t) cc_final: 0.8239 (p) REVERT: O 7 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.7941 (m) REVERT: O 17 SER cc_start: 0.8401 (p) cc_final: 0.8094 (m) outliers start: 86 outliers final: 43 residues processed: 408 average time/residue: 0.5960 time to fit residues: 271.3547 Evaluate side-chains 384 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 338 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 325 GLU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 69 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 0.0170 chunk 129 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 142 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 210 GLN A 290 ASN A 296 ASN ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN E 17 HIS E 44 GLN E 80 GLN E 152 ASN E 210 GLN E 285 ASN F 53 ASN F 125 GLN P 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.126317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115821 restraints weight = 23305.170| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.78 r_work: 0.3369 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16852 Z= 0.180 Angle : 0.541 11.550 22857 Z= 0.288 Chirality : 0.042 0.147 2463 Planarity : 0.005 0.052 2985 Dihedral : 4.734 34.511 2316 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.22 % Allowed : 26.22 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.18), residues: 2094 helix: 3.05 (0.25), residues: 360 sheet: 0.89 (0.21), residues: 579 loop : -1.36 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 62 TYR 0.013 0.001 TYR E 195 PHE 0.014 0.001 PHE B 24 TRP 0.020 0.001 TRP C 222 HIS 0.008 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00417 (16833) covalent geometry : angle 0.53802 (22821) SS BOND : bond 0.00488 ( 18) SS BOND : angle 1.53147 ( 36) hydrogen bonds : bond 0.04822 ( 672) hydrogen bonds : angle 4.81909 ( 1863) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 338 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 GLU cc_start: 0.7831 (mp0) cc_final: 0.7465 (mp0) REVERT: B 67 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 103 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7436 (mm-30) REVERT: B 128 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6257 (mp0) REVERT: C 34 ILE cc_start: 0.8519 (pt) cc_final: 0.8195 (mm) REVERT: C 126 THR cc_start: 0.8459 (m) cc_final: 0.8196 (t) REVERT: D 72 GLU cc_start: 0.7394 (mp0) cc_final: 0.6941 (mp0) REVERT: E 57 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7462 (ttm110) REVERT: E 114 SER cc_start: 0.8499 (t) cc_final: 0.8283 (m) REVERT: E 157 SER cc_start: 0.8396 (t) cc_final: 0.8192 (p) REVERT: E 182 VAL cc_start: 0.8355 (t) cc_final: 0.8141 (p) REVERT: F 131 GLU cc_start: 0.6731 (tt0) cc_final: 0.6434 (tt0) REVERT: F 168 ASN cc_start: 0.7990 (t0) cc_final: 0.7769 (t0) REVERT: O 17 SER cc_start: 0.8363 (p) cc_final: 0.8048 (m) outliers start: 76 outliers final: 39 residues processed: 386 average time/residue: 0.6087 time to fit residues: 262.2447 Evaluate side-chains 368 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 328 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 194 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 171 optimal weight: 0.0980 chunk 203 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 296 ASN B 116 ASN ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN E 44 GLN E 80 GLN E 152 ASN E 296 ASN F 53 ASN F 125 GLN P 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.113908 restraints weight = 23188.033| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.78 r_work: 0.3349 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16852 Z= 0.237 Angle : 0.575 11.974 22857 Z= 0.305 Chirality : 0.044 0.146 2463 Planarity : 0.005 0.054 2985 Dihedral : 4.713 35.078 2308 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.28 % Allowed : 26.50 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2094 helix: 3.04 (0.25), residues: 360 sheet: 0.92 (0.22), residues: 555 loop : -1.38 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 57 TYR 0.016 0.002 TYR E 195 PHE 0.018 0.002 PHE B 24 TRP 0.025 0.002 TRP C 222 HIS 0.009 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00551 (16833) covalent geometry : angle 0.57143 (22821) SS BOND : bond 0.00548 ( 18) SS BOND : angle 1.72404 ( 36) hydrogen bonds : bond 0.05047 ( 672) hydrogen bonds : angle 4.82200 ( 1863) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 360 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 261 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7895 (mtp85) REVERT: A 295 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: B 30 GLU cc_start: 0.7870 (mp0) cc_final: 0.7518 (mp0) REVERT: B 67 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7192 (mm-30) REVERT: B 103 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7454 (mm-30) REVERT: B 128 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6332 (mp0) REVERT: C 34 ILE cc_start: 0.8530 (pt) cc_final: 0.8218 (mm) REVERT: C 126 THR cc_start: 0.8433 (m) cc_final: 0.8164 (t) REVERT: D 17 MET cc_start: 0.8709 (tpp) cc_final: 0.8242 (ttp) REVERT: D 72 GLU cc_start: 0.7300 (mp0) cc_final: 0.6868 (mp0) REVERT: D 131 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7102 (tt0) REVERT: E 57 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7458 (ttm110) REVERT: E 114 SER cc_start: 0.8529 (t) cc_final: 0.8304 (m) REVERT: E 182 VAL cc_start: 0.8419 (t) cc_final: 0.8216 (p) REVERT: F 131 GLU cc_start: 0.6821 (tt0) cc_final: 0.6554 (tt0) REVERT: F 168 ASN cc_start: 0.8005 (t0) cc_final: 0.7778 (t0) REVERT: F 171 PHE cc_start: 0.7925 (m-80) cc_final: 0.7674 (m-80) REVERT: O 7 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.7938 (m) REVERT: O 17 SER cc_start: 0.8368 (p) cc_final: 0.8012 (m) outliers start: 77 outliers final: 49 residues processed: 409 average time/residue: 0.5829 time to fit residues: 266.1905 Evaluate side-chains 408 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 356 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 15 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 113 optimal weight: 0.1980 chunk 147 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 162 optimal weight: 0.0030 chunk 182 optimal weight: 0.5980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 169 ASN C 296 ASN D 125 GLN E 44 GLN E 152 ASN E 210 GLN E 296 ASN F 53 ASN F 125 GLN P 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116340 restraints weight = 23191.509| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.76 r_work: 0.3377 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16852 Z= 0.162 Angle : 0.531 11.320 22857 Z= 0.282 Chirality : 0.042 0.143 2463 Planarity : 0.005 0.050 2985 Dihedral : 4.507 33.269 2307 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.11 % Allowed : 26.28 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.18), residues: 2094 helix: 3.21 (0.25), residues: 360 sheet: 0.97 (0.22), residues: 561 loop : -1.36 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 57 TYR 0.013 0.001 TYR E 195 PHE 0.013 0.001 PHE B 24 TRP 0.020 0.001 TRP C 222 HIS 0.009 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00374 (16833) covalent geometry : angle 0.52714 (22821) SS BOND : bond 0.00573 ( 18) SS BOND : angle 1.63621 ( 36) hydrogen bonds : bond 0.04519 ( 672) hydrogen bonds : angle 4.65354 ( 1863) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 343 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7791 (mtp85) REVERT: B 30 GLU cc_start: 0.7885 (mp0) cc_final: 0.7488 (mp0) REVERT: B 67 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 103 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7394 (mm-30) REVERT: B 128 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6275 (mp0) REVERT: C 34 ILE cc_start: 0.8535 (pt) cc_final: 0.8201 (mm) REVERT: C 126 THR cc_start: 0.8421 (m) cc_final: 0.8140 (t) REVERT: D 17 MET cc_start: 0.8632 (tpp) cc_final: 0.8171 (ttp) REVERT: D 72 GLU cc_start: 0.7223 (mp0) cc_final: 0.6818 (mp0) REVERT: M 43 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7979 (mtmp) REVERT: E 57 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7491 (ttm110) REVERT: E 157 SER cc_start: 0.8413 (t) cc_final: 0.8188 (p) REVERT: E 182 VAL cc_start: 0.8373 (t) cc_final: 0.8154 (p) REVERT: F 131 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6433 (tt0) REVERT: F 168 ASN cc_start: 0.7994 (t0) cc_final: 0.7726 (t0) REVERT: F 171 PHE cc_start: 0.7897 (m-80) cc_final: 0.7612 (m-80) REVERT: O 7 SER cc_start: 0.8347 (OUTLIER) cc_final: 0.7906 (m) REVERT: O 17 SER cc_start: 0.8373 (p) cc_final: 0.8030 (m) outliers start: 74 outliers final: 47 residues processed: 391 average time/residue: 0.6208 time to fit residues: 270.1440 Evaluate side-chains 393 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 342 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 125 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 0.0000 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN E 44 GLN E 152 ASN E 216 ASN E 296 ASN F 53 ASN F 125 GLN P 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113989 restraints weight = 23236.142| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.78 r_work: 0.3366 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16852 Z= 0.184 Angle : 0.544 11.363 22857 Z= 0.288 Chirality : 0.042 0.145 2463 Planarity : 0.005 0.050 2985 Dihedral : 4.508 33.502 2305 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.50 % Allowed : 26.22 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2094 helix: 3.19 (0.25), residues: 360 sheet: 1.12 (0.22), residues: 528 loop : -1.40 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 57 TYR 0.014 0.001 TYR E 195 PHE 0.015 0.001 PHE B 24 TRP 0.022 0.001 TRP C 222 HIS 0.008 0.002 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00428 (16833) covalent geometry : angle 0.53865 (22821) SS BOND : bond 0.00525 ( 18) SS BOND : angle 1.92223 ( 36) hydrogen bonds : bond 0.04611 ( 672) hydrogen bonds : angle 4.62575 ( 1863) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 351 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.6904 (mtp85) REVERT: A 261 ARG cc_start: 0.8214 (mtp85) cc_final: 0.7821 (mtp85) REVERT: A 295 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: B 67 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7225 (mm-30) REVERT: B 103 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7469 (mm-30) REVERT: B 128 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6220 (mp0) REVERT: C 34 ILE cc_start: 0.8526 (pt) cc_final: 0.8192 (mm) REVERT: D 17 MET cc_start: 0.8629 (tpp) cc_final: 0.8185 (ttp) REVERT: D 72 GLU cc_start: 0.7256 (mp0) cc_final: 0.6839 (mp0) REVERT: M 43 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8027 (mtmp) REVERT: E 29 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8055 (mp) REVERT: E 57 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7449 (ttm110) REVERT: E 182 VAL cc_start: 0.8396 (t) cc_final: 0.8184 (p) REVERT: F 131 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6450 (tt0) REVERT: F 168 ASN cc_start: 0.8035 (t0) cc_final: 0.7773 (t0) REVERT: F 171 PHE cc_start: 0.7927 (m-80) cc_final: 0.7625 (m-80) REVERT: O 7 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.7925 (m) REVERT: O 17 SER cc_start: 0.8360 (p) cc_final: 0.8011 (m) outliers start: 81 outliers final: 54 residues processed: 404 average time/residue: 0.6206 time to fit residues: 278.9940 Evaluate side-chains 403 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 343 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 198 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 169 ASN D 125 GLN E 44 GLN E 152 ASN E 210 GLN E 216 ASN E 296 ASN F 53 ASN F 125 GLN P 38 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115479 restraints weight = 23122.192| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.77 r_work: 0.3362 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16852 Z= 0.208 Angle : 0.560 11.484 22857 Z= 0.297 Chirality : 0.043 0.152 2463 Planarity : 0.005 0.051 2985 Dihedral : 4.578 33.297 2304 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.89 % Allowed : 26.11 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.17 (0.18), residues: 2094 helix: 3.15 (0.25), residues: 360 sheet: 1.02 (0.21), residues: 546 loop : -1.42 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 57 TYR 0.014 0.002 TYR E 195 PHE 0.016 0.002 PHE B 24 TRP 0.023 0.001 TRP C 222 HIS 0.009 0.002 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00485 (16833) covalent geometry : angle 0.55412 (22821) SS BOND : bond 0.00561 ( 18) SS BOND : angle 2.06315 ( 36) hydrogen bonds : bond 0.04743 ( 672) hydrogen bonds : angle 4.66354 ( 1863) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 352 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.6909 (mtp85) REVERT: A 261 ARG cc_start: 0.8213 (mtp85) cc_final: 0.7802 (mtp85) REVERT: A 295 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: B 103 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7461 (mm-30) REVERT: C 34 ILE cc_start: 0.8519 (pt) cc_final: 0.8179 (mm) REVERT: D 17 MET cc_start: 0.8644 (tpp) cc_final: 0.8224 (ttp) REVERT: D 72 GLU cc_start: 0.7322 (mp0) cc_final: 0.6898 (mp0) REVERT: M 43 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8029 (mtmp) REVERT: E 29 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8049 (mp) REVERT: E 57 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7490 (ttm110) REVERT: E 157 SER cc_start: 0.8409 (t) cc_final: 0.8205 (p) REVERT: E 182 VAL cc_start: 0.8416 (t) cc_final: 0.8206 (p) REVERT: F 168 ASN cc_start: 0.8016 (t0) cc_final: 0.7747 (t0) REVERT: F 171 PHE cc_start: 0.7935 (m-80) cc_final: 0.7630 (m-80) REVERT: O 7 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.7929 (m) REVERT: O 17 SER cc_start: 0.8373 (p) cc_final: 0.8015 (m) outliers start: 88 outliers final: 63 residues processed: 411 average time/residue: 0.6261 time to fit residues: 285.9051 Evaluate side-chains 416 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 348 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 115 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 123 optimal weight: 0.5980 chunk 185 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 0.0870 chunk 92 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN C 44 GLN D 34 GLN D 125 GLN E 44 GLN E 152 ASN E 210 GLN E 216 ASN F 53 ASN F 125 GLN P 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116298 restraints weight = 23173.901| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.77 r_work: 0.3389 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16852 Z= 0.143 Angle : 0.519 10.866 22857 Z= 0.274 Chirality : 0.041 0.147 2463 Planarity : 0.005 0.048 2985 Dihedral : 4.363 36.227 2304 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.11 % Allowed : 26.72 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 2094 helix: 3.36 (0.25), residues: 360 sheet: 1.05 (0.21), residues: 546 loop : -1.34 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 57 TYR 0.012 0.001 TYR A 195 PHE 0.012 0.001 PHE B 24 TRP 0.018 0.001 TRP C 222 HIS 0.007 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00331 (16833) covalent geometry : angle 0.51455 (22821) SS BOND : bond 0.00475 ( 18) SS BOND : angle 1.69738 ( 36) hydrogen bonds : bond 0.04235 ( 672) hydrogen bonds : angle 4.48952 ( 1863) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 358 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7444 (ttm-80) cc_final: 0.6936 (mtp85) REVERT: A 261 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7764 (mtp85) REVERT: B 103 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7424 (mm-30) REVERT: B 128 GLU cc_start: 0.6904 (mp0) cc_final: 0.6541 (mp0) REVERT: C 34 ILE cc_start: 0.8520 (pt) cc_final: 0.8186 (mm) REVERT: D 17 MET cc_start: 0.8565 (tpp) cc_final: 0.8106 (ttp) REVERT: D 72 GLU cc_start: 0.7219 (mp0) cc_final: 0.6827 (mp0) REVERT: E 57 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7516 (ttm110) REVERT: E 157 SER cc_start: 0.8405 (t) cc_final: 0.8184 (p) REVERT: E 168 MET cc_start: 0.8347 (tpp) cc_final: 0.8118 (mmm) REVERT: E 182 VAL cc_start: 0.8387 (t) cc_final: 0.8171 (p) REVERT: E 208 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.7388 (mtm-85) REVERT: F 131 GLU cc_start: 0.6851 (tt0) cc_final: 0.6229 (tt0) REVERT: F 168 ASN cc_start: 0.8023 (t0) cc_final: 0.7742 (t0) REVERT: O 7 SER cc_start: 0.8351 (t) cc_final: 0.7922 (m) REVERT: O 17 SER cc_start: 0.8357 (p) cc_final: 0.8009 (m) outliers start: 74 outliers final: 54 residues processed: 404 average time/residue: 0.6114 time to fit residues: 274.3110 Evaluate side-chains 403 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 348 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain P residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 198 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 169 ASN D 125 GLN E 44 GLN E 152 ASN E 210 GLN E 216 ASN E 296 ASN F 53 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113776 restraints weight = 23315.178| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.78 r_work: 0.3354 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16852 Z= 0.254 Angle : 0.591 11.806 22857 Z= 0.313 Chirality : 0.044 0.161 2463 Planarity : 0.005 0.052 2985 Dihedral : 4.700 38.200 2304 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.11 % Allowed : 26.94 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2094 helix: 3.08 (0.25), residues: 360 sheet: 0.94 (0.21), residues: 546 loop : -1.44 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 57 TYR 0.016 0.002 TYR E 195 PHE 0.018 0.002 PHE B 24 TRP 0.024 0.002 TRP C 222 HIS 0.009 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00590 (16833) covalent geometry : angle 0.58475 (22821) SS BOND : bond 0.00631 ( 18) SS BOND : angle 2.23115 ( 36) hydrogen bonds : bond 0.04971 ( 672) hydrogen bonds : angle 4.69981 ( 1863) Misc. bond : bond 0.00074 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 350 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7751 (mtp85) REVERT: B 103 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7499 (mm-30) REVERT: B 128 GLU cc_start: 0.6906 (mp0) cc_final: 0.6506 (mp0) REVERT: C 34 ILE cc_start: 0.8527 (pt) cc_final: 0.8209 (mm) REVERT: D 17 MET cc_start: 0.8693 (tpp) cc_final: 0.8267 (ttp) REVERT: D 72 GLU cc_start: 0.7312 (mp0) cc_final: 0.6902 (mp0) REVERT: E 29 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8097 (mp) REVERT: E 57 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7495 (ttm110) REVERT: E 165 ASN cc_start: 0.7849 (t0) cc_final: 0.7647 (t0) REVERT: E 182 VAL cc_start: 0.8415 (t) cc_final: 0.8210 (p) REVERT: F 131 GLU cc_start: 0.6969 (tt0) cc_final: 0.6324 (tt0) REVERT: F 168 ASN cc_start: 0.8037 (t0) cc_final: 0.7765 (t0) REVERT: O 17 SER cc_start: 0.8398 (p) cc_final: 0.8014 (m) REVERT: O 82 MET cc_start: 0.7825 (mtm) cc_final: 0.7592 (mtt) outliers start: 74 outliers final: 52 residues processed: 400 average time/residue: 0.6087 time to fit residues: 271.0975 Evaluate side-chains 403 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 349 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain P residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 192 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 148 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN D 125 GLN E 44 GLN E 80 GLN E 152 ASN E 210 GLN E 216 ASN F 53 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113988 restraints weight = 23165.930| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.77 r_work: 0.3358 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16852 Z= 0.243 Angle : 0.587 11.661 22857 Z= 0.311 Chirality : 0.044 0.155 2463 Planarity : 0.005 0.051 2985 Dihedral : 4.681 39.751 2303 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.56 % Allowed : 27.78 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.18), residues: 2094 helix: 3.05 (0.25), residues: 360 sheet: 0.77 (0.21), residues: 579 loop : -1.42 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 57 TYR 0.015 0.002 TYR E 195 PHE 0.017 0.002 PHE B 24 TRP 0.023 0.002 TRP C 222 HIS 0.009 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00564 (16833) covalent geometry : angle 0.58102 (22821) SS BOND : bond 0.00602 ( 18) SS BOND : angle 2.22258 ( 36) hydrogen bonds : bond 0.04889 ( 672) hydrogen bonds : angle 4.71618 ( 1863) Misc. bond : bond 0.00066 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 342 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7347 (ttm-80) cc_final: 0.6977 (mtp180) REVERT: B 103 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7487 (mm-30) REVERT: B 128 GLU cc_start: 0.6944 (mp0) cc_final: 0.6551 (mp0) REVERT: C 34 ILE cc_start: 0.8527 (pt) cc_final: 0.8201 (mm) REVERT: D 17 MET cc_start: 0.8690 (tpp) cc_final: 0.8257 (ttp) REVERT: D 72 GLU cc_start: 0.7318 (mp0) cc_final: 0.6910 (mp0) REVERT: E 29 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8096 (mp) REVERT: E 57 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7479 (ttm110) REVERT: E 141 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7690 (mtt-85) REVERT: E 182 VAL cc_start: 0.8427 (t) cc_final: 0.8220 (p) REVERT: F 131 GLU cc_start: 0.7001 (tt0) cc_final: 0.6372 (tt0) REVERT: F 168 ASN cc_start: 0.8036 (t0) cc_final: 0.7764 (t0) REVERT: O 17 SER cc_start: 0.8416 (p) cc_final: 0.8022 (m) REVERT: O 82 MET cc_start: 0.7835 (mtm) cc_final: 0.7619 (mtt) outliers start: 64 outliers final: 53 residues processed: 384 average time/residue: 0.6536 time to fit residues: 278.0105 Evaluate side-chains 397 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 342 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 206 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 140 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN D 125 GLN E 80 GLN E 152 ASN E 210 GLN F 53 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114900 restraints weight = 23165.340| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.77 r_work: 0.3368 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16852 Z= 0.210 Angle : 0.570 11.455 22857 Z= 0.301 Chirality : 0.043 0.151 2463 Planarity : 0.005 0.050 2985 Dihedral : 4.625 44.674 2303 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.44 % Allowed : 27.83 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.18), residues: 2094 helix: 3.11 (0.25), residues: 360 sheet: 0.89 (0.21), residues: 546 loop : -1.43 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 57 TYR 0.014 0.002 TYR E 195 PHE 0.015 0.002 PHE B 24 TRP 0.022 0.001 TRP C 222 HIS 0.008 0.002 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00488 (16833) covalent geometry : angle 0.56376 (22821) SS BOND : bond 0.00561 ( 18) SS BOND : angle 2.11122 ( 36) hydrogen bonds : bond 0.04717 ( 672) hydrogen bonds : angle 4.66287 ( 1863) Misc. bond : bond 0.00050 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7667.33 seconds wall clock time: 131 minutes 39.06 seconds (7899.06 seconds total)