Starting phenix.real_space_refine on Thu Mar 5 03:50:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sjn_25162/03_2026/7sjn_25162.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sjn_25162/03_2026/7sjn_25162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sjn_25162/03_2026/7sjn_25162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sjn_25162/03_2026/7sjn_25162.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sjn_25162/03_2026/7sjn_25162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sjn_25162/03_2026/7sjn_25162.map" } resolution = 3.4 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= 0.005 sd= 0.078 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: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 6069 2.51 5 N 1611 2.21 5 O 1881 1.98 5 H 9483 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19062 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3012 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain breaks: 1 Chain: "B" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3012 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain breaks: 1 Chain: "C" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3012 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain breaks: 1 Chain: "D" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1764 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "E" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1578 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "F" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1764 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "G" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1578 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "H" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1764 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "L" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1578 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Time building chain proxies: 3.37, per 1000 atoms: 0.18 Number of scatterers: 19062 At special positions: 0 Unit cell: (136.8, 136.8, 98.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 1881 8.00 N 1611 7.00 C 6069 6.00 H 9483 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 467.4 milliseconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 25 sheets defined 8.8% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 170 through 180 removed outlier: 4.130A pdb=" N ASP A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.963A pdb=" N ILE A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 357 through 367 Processing helix chain 'C' and resid 171 through 179 removed outlier: 3.607A pdb=" N VAL C 175 " --> pdb=" O PHE C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 357 through 367 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 78 through 82 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.610A pdb=" N SER F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.592A pdb=" N PHE G 82 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.638A pdb=" N ASP H 31 " --> pdb=" O LYS H 28 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.714A pdb=" N GLU H 56 " --> pdb=" O PRO H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.021A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 203 removed outlier: 6.612A pdb=" N LEU A 188 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER A 203 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE A 186 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL A 228 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE A 242 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS A 255 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 296 removed outlier: 4.047A pdb=" N THR A 291 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 282 " --> pdb=" O PRO A 331 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 332 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA4, first strand: chain 'B' and resid 237 through 239 removed outlier: 3.795A pdb=" N PHE B 207 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS B 255 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE B 242 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 292 through 296 removed outlier: 3.506A pdb=" N ILE B 282 " --> pdb=" O PRO B 331 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 332 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR B 344 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE B 355 " --> pdb=" O THR B 344 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LYS B 346 " --> pdb=" O PHE B 353 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 353 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 199 through 203 removed outlier: 3.594A pdb=" N VAL C 199 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 188 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER C 203 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 186 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 199 through 203 removed outlier: 3.594A pdb=" N VAL C 199 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 188 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER C 203 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 186 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 207 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS C 255 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE C 242 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 292 through 296 removed outlier: 3.588A pdb=" N GLY C 341 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN C 334 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 339 " --> pdb=" O ASN C 334 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR C 344 " --> pdb=" O PHE C 353 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE C 353 " --> pdb=" O THR C 344 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LYS C 346 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE C 351 " --> pdb=" O LYS C 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.636A pdb=" N LEU D 83 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 11 removed outlier: 7.643A pdb=" N GLU D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.613A pdb=" N TYR D 95 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.909A pdb=" N LEU E 11 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TRP E 34 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 61 through 66 Processing sheet with id=AB6, first strand: chain 'E' and resid 88 through 89 removed outlier: 3.825A pdb=" N GLN E 89 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR E 96 " --> pdb=" O GLN E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.566A pdb=" N GLU F 10 " --> pdb=" O THR F 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 59 through 60 removed outlier: 5.328A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU F 33 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL F 93 " --> pdb=" O GLN F 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.564A pdb=" N VAL G 19 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 10 through 13 removed outlier: 7.012A pdb=" N LEU G 11 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA G 83 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP G 34 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 13 removed outlier: 7.012A pdb=" N LEU G 11 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA G 83 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN G 89 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR G 96 " --> pdb=" O GLN G 89 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.614A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 57 through 60 removed outlier: 4.378A pdb=" N GLY H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP H 52 " --> pdb=" O GLY H 57 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.639A pdb=" N PHE L 70 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.329A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 732 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: 3.79 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9483 1.02 - 1.22: 4 1.22 - 1.42: 4059 1.42 - 1.62: 5687 1.62 - 1.82: 24 Bond restraints: 19257 Sorted by residual: bond pdb=" ND2 ASN E 52 " pdb="HD21 ASN E 52 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN E 52 " pdb="HD22 ASN E 52 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" NE ARG B 197 " pdb=" HE ARG B 197 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" NE ARG B 166 " pdb=" HE ARG B 166 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG F 87 " pdb=" HE ARG F 87 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 ... (remaining 19252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 34556 2.34 - 4.68: 217 4.68 - 7.03: 33 7.03 - 9.37: 11 9.37 - 11.71: 4 Bond angle restraints: 34821 Sorted by residual: angle pdb=" C THR D 113 " pdb=" CA THR D 113 " pdb=" CB THR D 113 " ideal model delta sigma weight residual 111.17 101.46 9.71 1.54e+00 4.22e-01 3.97e+01 angle pdb=" C SER D 7 " pdb=" N GLY D 8 " pdb=" CA GLY D 8 " ideal model delta sigma weight residual 121.01 129.52 -8.51 1.42e+00 4.96e-01 3.59e+01 angle pdb=" N ARG B 190 " pdb=" CA ARG B 190 " pdb=" C ARG B 190 " ideal model delta sigma weight residual 111.04 102.80 8.24 1.55e+00 4.16e-01 2.82e+01 angle pdb=" N ALA D 58 " pdb=" CA ALA D 58 " pdb=" C ALA D 58 " ideal model delta sigma weight residual 108.76 117.59 -8.83 1.69e+00 3.50e-01 2.73e+01 angle pdb=" C LYS B 191 " pdb=" N LEU B 192 " pdb=" CA LEU B 192 " ideal model delta sigma weight residual 121.80 133.51 -11.71 2.44e+00 1.68e-01 2.30e+01 ... (remaining 34816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 8256 17.28 - 34.57: 637 34.57 - 51.85: 168 51.85 - 69.13: 41 69.13 - 86.42: 9 Dihedral angle restraints: 9111 sinusoidal: 4944 harmonic: 4167 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 43.28 49.72 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" C THR D 113 " pdb=" N THR D 113 " pdb=" CA THR D 113 " pdb=" CB THR D 113 " ideal model delta harmonic sigma weight residual -122.00 -109.47 -12.53 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" N LYS B 196 " pdb=" C LYS B 196 " pdb=" CA LYS B 196 " pdb=" CB LYS B 196 " ideal model delta harmonic sigma weight residual 122.80 133.94 -11.14 0 2.50e+00 1.60e-01 1.99e+01 ... (remaining 9108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1317 0.072 - 0.143: 189 0.143 - 0.215: 8 0.215 - 0.286: 3 0.286 - 0.358: 1 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CA LYS B 196 " pdb=" N LYS B 196 " pdb=" C LYS B 196 " pdb=" CB LYS B 196 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA THR D 113 " pdb=" N THR D 113 " pdb=" C THR D 113 " pdb=" CB THR D 113 " both_signs ideal model delta sigma weight residual False 2.53 2.79 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA SER B 195 " pdb=" N SER B 195 " pdb=" C SER B 195 " pdb=" CB SER B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1515 not shown) Planarity restraints: 2871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 194 " 0.023 2.00e-02 2.50e+03 4.38e-02 1.91e+01 pdb=" N SER B 195 " -0.075 2.00e-02 2.50e+03 pdb=" CA SER B 195 " 0.018 2.00e-02 2.50e+03 pdb=" H SER B 195 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 3 " 0.032 2.00e-02 2.50e+03 3.47e-02 1.81e+01 pdb=" CD GLN H 3 " -0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN H 3 " -0.031 2.00e-02 2.50e+03 pdb=" NE2 GLN H 3 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN H 3 " -0.051 2.00e-02 2.50e+03 pdb="HE22 GLN H 3 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 3 " -0.030 2.00e-02 2.50e+03 3.18e-02 1.52e+01 pdb=" CD GLN L 3 " 0.003 2.00e-02 2.50e+03 pdb=" OE1 GLN L 3 " 0.028 2.00e-02 2.50e+03 pdb=" NE2 GLN L 3 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN L 3 " -0.048 2.00e-02 2.50e+03 pdb="HE22 GLN L 3 " 0.046 2.00e-02 2.50e+03 ... (remaining 2868 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 744 2.17 - 2.77: 37471 2.77 - 3.38: 49626 3.38 - 3.99: 66222 3.99 - 4.60: 102224 Nonbonded interactions: 256287 Sorted by model distance: nonbonded pdb=" HB2 PRO B 193 " pdb=" HZ2 TRP E 95 " model vdw 1.557 2.270 nonbonded pdb=" OD1 ASP D 101 " pdb=" H TYR D 102 " model vdw 1.601 2.450 nonbonded pdb=" O CYS D 96 " pdb=" H GLY D 110 " model vdw 1.636 2.450 nonbonded pdb="HH11 ARG B 190 " pdb=" HE1 TYR D 100 " model vdw 1.643 2.100 nonbonded pdb="HH21 ARG B 227 " pdb=" OD2 ASP D 101 " model vdw 1.646 2.450 ... (remaining 256282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } 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: 1.550 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.660 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.004 0.088 9780 Z= 0.213 Angle : 0.650 11.712 13275 Z= 0.385 Chirality : 0.049 0.358 1518 Planarity : 0.004 0.085 1692 Dihedral : 12.762 86.418 3528 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 8.77 % 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: -0.44 (0.26), residues: 1227 helix: 1.42 (0.73), residues: 66 sheet: -0.49 (0.24), residues: 520 loop : -0.16 (0.27), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 197 TYR 0.010 0.001 TYR E 35 PHE 0.018 0.001 PHE L 97 TRP 0.040 0.002 TRP G 95 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9774) covalent geometry : angle 0.64884 (13263) SS BOND : bond 0.00733 ( 6) SS BOND : angle 1.21457 ( 12) hydrogen bonds : bond 0.18522 ( 291) hydrogen bonds : angle 7.98350 ( 732) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 70 ILE cc_start: 0.8209 (mm) cc_final: 0.7601 (mm) REVERT: D 73 ASP cc_start: 0.6245 (t0) cc_final: 0.5893 (t0) REVERT: D 116 THR cc_start: 0.8581 (m) cc_final: 0.8347 (p) REVERT: E 4 MET cc_start: 0.6851 (mtp) cc_final: 0.5555 (mtp) REVERT: F 47 TRP cc_start: 0.7317 (t60) cc_final: 0.6602 (t60) REVERT: G 96 THR cc_start: 0.8058 (p) cc_final: 0.7722 (t) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2488 time to fit residues: 66.7304 Evaluate side-chains 143 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN D 6 GLN D 111 GLN E 33 HIS E 88 GLN E 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.178322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.125695 restraints weight = 42907.317| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.12 r_work: 0.3601 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9780 Z= 0.139 Angle : 0.519 4.603 13275 Z= 0.277 Chirality : 0.046 0.157 1518 Planarity : 0.003 0.045 1692 Dihedral : 3.996 16.228 1329 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.38 % Allowed : 7.77 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.42 (0.25), residues: 1227 helix: 1.56 (0.72), residues: 66 sheet: -0.51 (0.23), residues: 525 loop : -0.13 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 269 TYR 0.009 0.001 TYR D 108 PHE 0.011 0.001 PHE L 82 TRP 0.018 0.001 TRP G 90 HIS 0.004 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9774) covalent geometry : angle 0.51802 (13263) SS BOND : bond 0.00432 ( 6) SS BOND : angle 1.26892 ( 12) hydrogen bonds : bond 0.04038 ( 291) hydrogen bonds : angle 6.10762 ( 732) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 LYS cc_start: 0.8468 (tptt) cc_final: 0.8034 (tptm) REVERT: D 73 ASP cc_start: 0.6356 (t0) cc_final: 0.5965 (t0) REVERT: D 90 ASP cc_start: 0.7185 (t0) cc_final: 0.6859 (m-30) REVERT: E 21 ILE cc_start: 0.7949 (mt) cc_final: 0.7702 (tp) REVERT: F 47 TRP cc_start: 0.7608 (t60) cc_final: 0.6947 (t60) REVERT: F 103 ASP cc_start: 0.8475 (m-30) cc_final: 0.8240 (m-30) REVERT: G 4 MET cc_start: 0.8804 (mmp) cc_final: 0.8508 (mmp) outliers start: 4 outliers final: 3 residues processed: 174 average time/residue: 0.2583 time to fit residues: 59.5589 Evaluate side-chains 150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain E residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 12 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.160736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114425 restraints weight = 41488.098| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.44 r_work: 0.3309 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9780 Z= 0.159 Angle : 0.520 6.246 13275 Z= 0.274 Chirality : 0.046 0.160 1518 Planarity : 0.003 0.028 1692 Dihedral : 4.020 21.126 1329 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.42 % Allowed : 9.09 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.42 (0.25), residues: 1227 helix: 1.27 (0.69), residues: 72 sheet: -0.52 (0.24), residues: 503 loop : -0.12 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 269 TYR 0.011 0.001 TYR E 35 PHE 0.011 0.001 PHE A 207 TRP 0.018 0.002 TRP E 95 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9774) covalent geometry : angle 0.51934 (13263) SS BOND : bond 0.00568 ( 6) SS BOND : angle 1.14436 ( 12) hydrogen bonds : bond 0.03831 ( 291) hydrogen bonds : angle 5.72957 ( 732) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LYS cc_start: 0.6577 (ttmm) cc_final: 0.6170 (ttpt) REVERT: D 48 ILE cc_start: 0.7362 (mt) cc_final: 0.6892 (mt) REVERT: D 70 ILE cc_start: 0.7570 (mm) cc_final: 0.7119 (mm) REVERT: D 73 ASP cc_start: 0.6401 (t0) cc_final: 0.6174 (t0) REVERT: D 90 ASP cc_start: 0.7236 (t0) cc_final: 0.7018 (m-30) REVERT: E 44 LYS cc_start: 0.7648 (mmmm) cc_final: 0.7184 (tptp) REVERT: E 88 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6959 (tp-100) REVERT: F 47 TRP cc_start: 0.7993 (t60) cc_final: 0.7616 (t60) REVERT: G 4 MET cc_start: 0.8689 (mmp) cc_final: 0.8385 (mmp) outliers start: 15 outliers final: 12 residues processed: 159 average time/residue: 0.2640 time to fit residues: 55.6381 Evaluate side-chains 159 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 104 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.177980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.125259 restraints weight = 42786.508| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.18 r_work: 0.3566 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9780 Z= 0.150 Angle : 0.501 5.040 13275 Z= 0.264 Chirality : 0.046 0.159 1518 Planarity : 0.003 0.029 1692 Dihedral : 4.003 22.945 1329 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.04 % Allowed : 10.80 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.25), residues: 1227 helix: 1.27 (0.69), residues: 72 sheet: -0.49 (0.24), residues: 498 loop : -0.16 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 269 TYR 0.010 0.001 TYR E 35 PHE 0.011 0.001 PHE A 207 TRP 0.020 0.001 TRP G 90 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9774) covalent geometry : angle 0.50044 (13263) SS BOND : bond 0.00525 ( 6) SS BOND : angle 1.00339 ( 12) hydrogen bonds : bond 0.03450 ( 291) hydrogen bonds : angle 5.47587 ( 732) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LYS cc_start: 0.6708 (ttmm) cc_final: 0.6271 (ttpt) REVERT: D 47 TRP cc_start: 0.7856 (t60) cc_final: 0.7570 (t60) REVERT: D 48 ILE cc_start: 0.7415 (mt) cc_final: 0.6701 (mt) REVERT: D 73 ASP cc_start: 0.6525 (t0) cc_final: 0.6229 (t0) REVERT: D 90 ASP cc_start: 0.7281 (t0) cc_final: 0.6901 (m-30) REVERT: E 88 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6916 (tp-100) REVERT: F 47 TRP cc_start: 0.7667 (t60) cc_final: 0.7182 (t60) REVERT: F 101 ASP cc_start: 0.8140 (t0) cc_final: 0.7887 (t0) REVERT: G 4 MET cc_start: 0.8582 (mmp) cc_final: 0.8267 (mmp) outliers start: 11 outliers final: 10 residues processed: 164 average time/residue: 0.2642 time to fit residues: 56.8197 Evaluate side-chains 157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 94 optimal weight: 0.0470 chunk 63 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 GLN D 111 GLN F 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.178190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125864 restraints weight = 42671.563| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.16 r_work: 0.3577 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9780 Z= 0.120 Angle : 0.476 4.573 13275 Z= 0.249 Chirality : 0.045 0.157 1518 Planarity : 0.003 0.054 1692 Dihedral : 3.899 23.910 1329 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.14 % Allowed : 12.22 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.28 (0.25), residues: 1227 helix: 1.37 (0.69), residues: 72 sheet: -0.44 (0.23), residues: 513 loop : 0.01 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 269 TYR 0.008 0.001 TYR F 95 PHE 0.009 0.001 PHE A 207 TRP 0.015 0.001 TRP G 90 HIS 0.003 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9774) covalent geometry : angle 0.47574 (13263) SS BOND : bond 0.00493 ( 6) SS BOND : angle 0.96553 ( 12) hydrogen bonds : bond 0.03140 ( 291) hydrogen bonds : angle 5.26580 ( 732) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 LYS cc_start: 0.8434 (tptt) cc_final: 0.7994 (tptm) REVERT: D 28 LYS cc_start: 0.6744 (ttmm) cc_final: 0.6374 (ttpt) REVERT: D 73 ASP cc_start: 0.6489 (t0) cc_final: 0.6241 (t0) REVERT: D 90 ASP cc_start: 0.7251 (t0) cc_final: 0.6860 (m-30) REVERT: E 88 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6912 (tp-100) REVERT: F 47 TRP cc_start: 0.7655 (t60) cc_final: 0.7153 (t60) REVERT: F 101 ASP cc_start: 0.8175 (t0) cc_final: 0.7943 (t0) REVERT: G 4 MET cc_start: 0.8531 (mmp) cc_final: 0.8244 (mmp) REVERT: H 19 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7888 (pttp) REVERT: L 104 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6692 (pm20) outliers start: 12 outliers final: 8 residues processed: 157 average time/residue: 0.2535 time to fit residues: 52.6493 Evaluate side-chains 152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain L residue 104 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 84 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 116 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.176627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124028 restraints weight = 42685.703| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.19 r_work: 0.3544 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9780 Z= 0.149 Angle : 0.492 4.649 13275 Z= 0.258 Chirality : 0.046 0.164 1518 Planarity : 0.003 0.035 1692 Dihedral : 3.957 24.941 1329 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.52 % Allowed : 12.22 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.36 (0.25), residues: 1227 helix: 1.25 (0.69), residues: 72 sheet: -0.46 (0.23), residues: 513 loop : -0.06 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.010 0.001 TYR F 95 PHE 0.011 0.001 PHE A 207 TRP 0.023 0.001 TRP G 90 HIS 0.004 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9774) covalent geometry : angle 0.49163 (13263) SS BOND : bond 0.00538 ( 6) SS BOND : angle 0.94746 ( 12) hydrogen bonds : bond 0.03231 ( 291) hydrogen bonds : angle 5.24226 ( 732) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LYS cc_start: 0.6964 (ttmm) cc_final: 0.6524 (ttpt) REVERT: D 73 ASP cc_start: 0.6352 (t0) cc_final: 0.6119 (t0) REVERT: D 90 ASP cc_start: 0.7325 (t0) cc_final: 0.7012 (m-30) REVERT: D 103 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: E 88 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7108 (tp-100) REVERT: F 47 TRP cc_start: 0.7714 (t60) cc_final: 0.7225 (t60) REVERT: F 101 ASP cc_start: 0.8245 (t0) cc_final: 0.7957 (t0) REVERT: L 104 GLU cc_start: 0.6949 (pm20) cc_final: 0.6712 (pm20) outliers start: 16 outliers final: 12 residues processed: 153 average time/residue: 0.2514 time to fit residues: 51.4711 Evaluate side-chains 155 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 GLN D 111 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.176545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.124034 restraints weight = 43039.681| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.21 r_work: 0.3548 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9780 Z= 0.128 Angle : 0.484 4.639 13275 Z= 0.253 Chirality : 0.045 0.156 1518 Planarity : 0.003 0.033 1692 Dihedral : 3.914 23.904 1329 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.42 % Allowed : 13.16 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.25), residues: 1227 helix: 1.32 (0.69), residues: 72 sheet: -0.46 (0.23), residues: 513 loop : -0.05 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.008 0.001 TYR F 95 PHE 0.010 0.001 PHE A 207 TRP 0.014 0.001 TRP G 90 HIS 0.003 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9774) covalent geometry : angle 0.48321 (13263) SS BOND : bond 0.00547 ( 6) SS BOND : angle 0.88324 ( 12) hydrogen bonds : bond 0.03032 ( 291) hydrogen bonds : angle 5.13476 ( 732) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 GLN cc_start: 0.8374 (mm110) cc_final: 0.7677 (mm110) REVERT: D 28 LYS cc_start: 0.6998 (ttmm) cc_final: 0.6603 (ttpt) REVERT: D 73 ASP cc_start: 0.6283 (t0) cc_final: 0.5949 (t0) REVERT: D 90 ASP cc_start: 0.7329 (t0) cc_final: 0.7006 (m-30) REVERT: E 88 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7168 (tp-100) REVERT: F 47 TRP cc_start: 0.7746 (t60) cc_final: 0.7286 (t60) REVERT: F 101 ASP cc_start: 0.8200 (t0) cc_final: 0.7868 (t0) REVERT: G 4 MET cc_start: 0.8984 (mmp) cc_final: 0.8250 (mmp) REVERT: L 104 GLU cc_start: 0.6964 (pm20) cc_final: 0.6704 (pm20) outliers start: 15 outliers final: 12 residues processed: 148 average time/residue: 0.2513 time to fit residues: 49.3837 Evaluate side-chains 152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.175517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.123222 restraints weight = 42882.447| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.18 r_work: 0.3539 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9780 Z= 0.161 Angle : 0.500 4.751 13275 Z= 0.262 Chirality : 0.046 0.159 1518 Planarity : 0.003 0.029 1692 Dihedral : 3.990 23.740 1329 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.42 % Allowed : 14.02 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.25), residues: 1227 helix: 1.25 (0.69), residues: 72 sheet: -0.46 (0.23), residues: 534 loop : -0.06 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 72 TYR 0.010 0.001 TYR F 95 PHE 0.012 0.001 PHE A 207 TRP 0.023 0.002 TRP G 90 HIS 0.004 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9774) covalent geometry : angle 0.49908 (13263) SS BOND : bond 0.00581 ( 6) SS BOND : angle 0.98670 ( 12) hydrogen bonds : bond 0.03176 ( 291) hydrogen bonds : angle 5.17670 ( 732) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 GLN cc_start: 0.8401 (mm110) cc_final: 0.7589 (mp10) REVERT: D 28 LYS cc_start: 0.7045 (ttmm) cc_final: 0.6608 (ttpt) REVERT: D 73 ASP cc_start: 0.6423 (t0) cc_final: 0.6074 (t0) REVERT: D 90 ASP cc_start: 0.7419 (t0) cc_final: 0.7053 (m-30) REVERT: D 103 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: D 111 GLN cc_start: 0.6209 (OUTLIER) cc_final: 0.5547 (tp-100) REVERT: E 41 LYS cc_start: 0.5474 (tptp) cc_final: 0.5143 (tptp) REVERT: E 85 TYR cc_start: 0.7371 (m-80) cc_final: 0.7123 (m-80) REVERT: E 88 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7052 (tp-100) REVERT: F 47 TRP cc_start: 0.7649 (t60) cc_final: 0.7104 (t60) REVERT: F 101 ASP cc_start: 0.8152 (t0) cc_final: 0.7785 (t0) REVERT: H 23 LYS cc_start: 0.7505 (mttt) cc_final: 0.7176 (pttm) REVERT: L 104 GLU cc_start: 0.6935 (pm20) cc_final: 0.6650 (pm20) outliers start: 15 outliers final: 12 residues processed: 149 average time/residue: 0.2369 time to fit residues: 47.2401 Evaluate side-chains 153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 20 optimal weight: 0.5980 chunk 90 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 69 optimal weight: 0.2980 chunk 85 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN F 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.176924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.129145 restraints weight = 42761.772| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.17 r_work: 0.3566 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9780 Z= 0.107 Angle : 0.479 4.535 13275 Z= 0.249 Chirality : 0.046 0.154 1518 Planarity : 0.003 0.029 1692 Dihedral : 3.842 24.034 1329 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.23 % Allowed : 14.11 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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 (0.25), residues: 1227 helix: 0.98 (0.67), residues: 78 sheet: -0.43 (0.23), residues: 519 loop : 0.04 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 72 TYR 0.010 0.001 TYR F 80 PHE 0.008 0.001 PHE A 207 TRP 0.013 0.001 TRP G 90 HIS 0.003 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9774) covalent geometry : angle 0.47820 (13263) SS BOND : bond 0.00494 ( 6) SS BOND : angle 0.94648 ( 12) hydrogen bonds : bond 0.02893 ( 291) hydrogen bonds : angle 5.01794 ( 732) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 GLN cc_start: 0.8369 (mm110) cc_final: 0.7543 (mp10) REVERT: D 23 LYS cc_start: 0.8432 (tptt) cc_final: 0.8067 (tptm) REVERT: D 28 LYS cc_start: 0.7135 (ttmm) cc_final: 0.6696 (ttpt) REVERT: D 73 ASP cc_start: 0.6458 (t0) cc_final: 0.6107 (t0) REVERT: D 90 ASP cc_start: 0.7428 (t0) cc_final: 0.7103 (m-30) REVERT: D 103 ASP cc_start: 0.8285 (t0) cc_final: 0.8067 (m-30) REVERT: E 41 LYS cc_start: 0.5451 (tptp) cc_final: 0.5190 (tptp) REVERT: E 44 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7689 (mmmt) REVERT: E 85 TYR cc_start: 0.7503 (m-80) cc_final: 0.7256 (m-80) REVERT: E 88 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7106 (tp-100) REVERT: F 47 TRP cc_start: 0.7852 (t60) cc_final: 0.7354 (t60) REVERT: F 101 ASP cc_start: 0.8302 (t0) cc_final: 0.7954 (t0) REVERT: G 4 MET cc_start: 0.8957 (mmp) cc_final: 0.8242 (mmp) REVERT: H 23 LYS cc_start: 0.7525 (mttt) cc_final: 0.7149 (pttm) REVERT: L 104 GLU cc_start: 0.6929 (pm20) cc_final: 0.6636 (pm20) outliers start: 13 outliers final: 12 residues processed: 153 average time/residue: 0.2463 time to fit residues: 50.0022 Evaluate side-chains 155 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 0.1980 chunk 114 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.176593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.123924 restraints weight = 42837.040| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.24 r_work: 0.3535 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9780 Z= 0.123 Angle : 0.489 4.887 13275 Z= 0.255 Chirality : 0.045 0.157 1518 Planarity : 0.003 0.048 1692 Dihedral : 3.877 24.010 1329 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.23 % Allowed : 13.83 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.25), residues: 1227 helix: 0.95 (0.67), residues: 78 sheet: -0.41 (0.23), residues: 516 loop : -0.01 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 87 TYR 0.012 0.001 TYR F 80 PHE 0.010 0.001 PHE A 207 TRP 0.019 0.001 TRP G 90 HIS 0.004 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9774) covalent geometry : angle 0.48879 (13263) SS BOND : bond 0.00537 ( 6) SS BOND : angle 0.91246 ( 12) hydrogen bonds : bond 0.02943 ( 291) hydrogen bonds : angle 5.02757 ( 732) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 GLN cc_start: 0.8323 (mm110) cc_final: 0.7531 (mp10) REVERT: D 23 LYS cc_start: 0.8382 (tptt) cc_final: 0.8035 (tptm) REVERT: D 28 LYS cc_start: 0.7142 (ttmm) cc_final: 0.6707 (ttpt) REVERT: D 73 ASP cc_start: 0.6804 (t0) cc_final: 0.6488 (t0) REVERT: D 90 ASP cc_start: 0.7402 (t0) cc_final: 0.7100 (m-30) REVERT: D 103 ASP cc_start: 0.8164 (t0) cc_final: 0.7935 (m-30) REVERT: E 41 LYS cc_start: 0.5551 (tptp) cc_final: 0.5291 (tptp) REVERT: E 44 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7721 (mmmt) REVERT: E 85 TYR cc_start: 0.7390 (m-80) cc_final: 0.7158 (m-80) REVERT: E 88 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7110 (tp-100) REVERT: F 101 ASP cc_start: 0.8193 (t0) cc_final: 0.7867 (t0) REVERT: G 4 MET cc_start: 0.8911 (mmp) cc_final: 0.8163 (mmp) REVERT: H 23 LYS cc_start: 0.7665 (mttt) cc_final: 0.7304 (pttm) REVERT: H 31 ASP cc_start: 0.7582 (m-30) cc_final: 0.7369 (m-30) REVERT: L 104 GLU cc_start: 0.6966 (pm20) cc_final: 0.6677 (pm20) outliers start: 13 outliers final: 11 residues processed: 150 average time/residue: 0.2433 time to fit residues: 48.7554 Evaluate side-chains 153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 34 optimal weight: 0.0970 chunk 90 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.176407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124174 restraints weight = 42848.750| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.19 r_work: 0.3554 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9780 Z= 0.118 Angle : 0.488 5.261 13275 Z= 0.254 Chirality : 0.046 0.156 1518 Planarity : 0.003 0.029 1692 Dihedral : 3.851 24.373 1329 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.14 % Allowed : 14.02 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1227 helix: 0.97 (0.67), residues: 78 sheet: -0.40 (0.23), residues: 516 loop : -0.01 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 87 TYR 0.010 0.001 TYR F 80 PHE 0.009 0.001 PHE A 207 TRP 0.017 0.001 TRP G 90 HIS 0.003 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9774) covalent geometry : angle 0.48691 (13263) SS BOND : bond 0.00500 ( 6) SS BOND : angle 0.94944 ( 12) hydrogen bonds : bond 0.02931 ( 291) hydrogen bonds : angle 4.99835 ( 732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4925.48 seconds wall clock time: 85 minutes 0.99 seconds (5100.99 seconds total)