Starting phenix.real_space_refine on Sat May 17 17:19:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vhx_43243/05_2025/8vhx_43243.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vhx_43243/05_2025/8vhx_43243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vhx_43243/05_2025/8vhx_43243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vhx_43243/05_2025/8vhx_43243.map" model { file = "/net/cci-nas-00/data/ceres_data/8vhx_43243/05_2025/8vhx_43243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vhx_43243/05_2025/8vhx_43243.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.041 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 81 5.16 5 C 10089 2.51 5 N 2788 2.21 5 O 3097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 151 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16055 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "B" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "C" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1316 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 154} Chain: "D" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3789 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 24, 'TRANS': 454} Chain breaks: 1 Chain: "E" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3789 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 24, 'TRANS': 454} Chain breaks: 1 Chain: "F" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "G" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2138 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 266} Chain: "H" Number of atoms: 2788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2788 Classifications: {'peptide': 375} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 363} Time building chain proxies: 12.02, per 1000 atoms: 0.75 Number of scatterers: 16055 At special positions: 0 Unit cell: (103.32, 134.48, 289.46, 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 81 16.00 O 3097 8.00 N 2788 7.00 C 10089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.75 Conformation dependent library (CDL) restraints added in 2.1 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3782 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 27 sheets defined 35.8% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 2 through 27 Processing helix chain 'A' and resid 47 through 64 Processing helix chain 'A' and resid 66 through 73 removed outlier: 4.387A pdb=" N MET A 72 " --> pdb=" O CYS A 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 47 through 64 Processing helix chain 'B' and resid 66 through 73 removed outlier: 4.099A pdb=" N MET B 72 " --> pdb=" O CYS B 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 17 through 18 No H-bonds generated for 'chain 'C' and resid 17 through 18' Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 65 through 68 Processing helix chain 'C' and resid 91 through 107 removed outlier: 3.980A pdb=" N TYR C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET C 107 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.990A pdb=" N GLY C 127 " --> pdb=" O TYR C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 42 removed outlier: 3.807A pdb=" N GLU D 42 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 80 through 95 Processing helix chain 'D' and resid 115 through 133 removed outlier: 3.532A pdb=" N GLU D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 162 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 235 through 238 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.869A pdb=" N ALA D 274 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 299 removed outlier: 3.513A pdb=" N TYR D 299 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'D' and resid 402 through 424 removed outlier: 3.745A pdb=" N TYR D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 444 Processing helix chain 'D' and resid 455 through 458 Processing helix chain 'D' and resid 459 through 468 Processing helix chain 'D' and resid 483 through 494 Processing helix chain 'D' and resid 498 through 506 Processing helix chain 'D' and resid 509 through 528 Processing helix chain 'E' and resid 57 through 65 Processing helix chain 'E' and resid 66 through 80 Processing helix chain 'E' and resid 80 through 95 Processing helix chain 'E' and resid 106 through 111 Processing helix chain 'E' and resid 116 through 133 removed outlier: 3.570A pdb=" N VAL E 131 " --> pdb=" O ARG E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 162 Processing helix chain 'E' and resid 176 through 180 Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 197 through 201 Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.765A pdb=" N GLN E 237 " --> pdb=" O ASP E 234 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP E 238 " --> pdb=" O LEU E 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 238' Processing helix chain 'E' and resid 270 through 274 Processing helix chain 'E' and resid 275 through 299 removed outlier: 3.733A pdb=" N TYR E 299 " --> pdb=" O VAL E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 317 Processing helix chain 'E' and resid 373 through 388 removed outlier: 3.599A pdb=" N SER E 386 " --> pdb=" O ASN E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 396 Processing helix chain 'E' and resid 402 through 424 Processing helix chain 'E' and resid 424 through 444 Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 459 through 468 removed outlier: 3.765A pdb=" N LEU E 466 " --> pdb=" O LYS E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 494 Processing helix chain 'E' and resid 498 through 506 Processing helix chain 'E' and resid 509 through 528 removed outlier: 3.517A pdb=" N VAL E 513 " --> pdb=" O ASP E 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 21 Processing helix chain 'F' and resid 71 through 78 Processing helix chain 'G' and resid 81 through 89 Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'H' and resid 81 through 89 Processing helix chain 'H' and resid 152 through 156 Processing helix chain 'H' and resid 367 through 369 No H-bonds generated for 'chain 'H' and resid 367 through 369' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 4.743A pdb=" N SER A 29 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU B 42 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL A 33 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG B 40 " --> pdb=" O VAL A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 82 removed outlier: 6.479A pdb=" N GLY B 80 " --> pdb=" O ILE E 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.655A pdb=" N LEU C 160 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.655A pdb=" N LEU C 160 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE C 151 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 140 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 100 through 103 Processing sheet with id=AA7, first strand: chain 'D' and resid 185 through 189 Processing sheet with id=AA8, first strand: chain 'D' and resid 207 through 208 removed outlier: 3.741A pdb=" N GLY D 221 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 301 through 304 Processing sheet with id=AB1, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB2, first strand: chain 'E' and resid 100 through 103 Processing sheet with id=AB3, first strand: chain 'E' and resid 188 through 189 Processing sheet with id=AB4, first strand: chain 'E' and resid 207 through 208 Processing sheet with id=AB5, first strand: chain 'F' and resid 22 through 27 removed outlier: 5.977A pdb=" N VAL F 22 " --> pdb=" O SER F 39 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER F 39 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA F 24 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER F 39 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR F 70 " --> pdb=" O SER F 39 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY F 63 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG F 119 " --> pdb=" O GLY F 63 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU F 65 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL F 114 " --> pdb=" O GLN F 104 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLN F 104 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN F 116 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 31 through 33 removed outlier: 6.604A pdb=" N VAL G 213 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER G 237 " --> pdb=" O VAL G 213 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY G 215 " --> pdb=" O LYS G 235 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS G 235 " --> pdb=" O GLY G 215 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER G 221 " --> pdb=" O LYS G 229 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LYS G 229 " --> pdb=" O SER G 221 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER G 255 " --> pdb=" O ASP G 241 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN G 71 " --> pdb=" O ALA G 260 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL G 65 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU G 47 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA G 69 " --> pdb=" O ASP G 45 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP G 45 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 39 through 41 removed outlier: 4.226A pdb=" N GLU G 39 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN G 71 " --> pdb=" O ALA G 260 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER G 255 " --> pdb=" O ASP G 241 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 92 through 97 Processing sheet with id=AB9, first strand: chain 'G' and resid 101 through 108 removed outlier: 3.579A pdb=" N ASP G 103 " --> pdb=" O TYR G 196 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N TYR G 196 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS G 105 " --> pdb=" O VAL G 194 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 194 " --> pdb=" O LYS G 105 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL G 107 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE G 192 " --> pdb=" O VAL G 107 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASP G 197 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ASN G 134 " --> pdb=" O ASP G 197 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N MET G 137 " --> pdb=" O VAL G 162 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 116 through 118 Processing sheet with id=AC2, first strand: chain 'H' and resid 28 through 33 removed outlier: 4.444A pdb=" N GLY H 30 " --> pdb=" O ARG H 20 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG H 20 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR H 214 " --> pdb=" O PHE H 21 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL H 213 " --> pdb=" O SER H 237 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER H 237 " --> pdb=" O VAL H 213 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY H 215 " --> pdb=" O LYS H 235 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS H 235 " --> pdb=" O GLY H 215 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 221 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS H 229 " --> pdb=" O SER H 221 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER H 255 " --> pdb=" O ASP H 241 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU H 39 " --> pdb=" O THR H 76 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 28 through 33 removed outlier: 4.444A pdb=" N GLY H 30 " --> pdb=" O ARG H 20 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG H 20 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR H 214 " --> pdb=" O PHE H 21 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL H 213 " --> pdb=" O SER H 237 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER H 237 " --> pdb=" O VAL H 213 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY H 215 " --> pdb=" O LYS H 235 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS H 235 " --> pdb=" O GLY H 215 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 221 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS H 229 " --> pdb=" O SER H 221 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN H 228 " --> pdb=" O VAL H 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 45 through 52 removed outlier: 6.087A pdb=" N ASP H 45 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA H 69 " --> pdb=" O ASP H 45 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU H 47 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 92 through 98 removed outlier: 3.788A pdb=" N GLN H 201 " --> pdb=" O GLN H 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 101 through 108 removed outlier: 5.591A pdb=" N THR H 102 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL H 198 " --> pdb=" O THR H 102 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP H 197 " --> pdb=" O ASN H 134 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN H 134 " --> pdb=" O ASP H 197 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 115 through 118 removed outlier: 3.710A pdb=" N ARG H 115 " --> pdb=" O ILE H 179 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 288 through 293 removed outlier: 3.572A pdb=" N THR H 349 " --> pdb=" O CYS H 307 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 297 through 299 removed outlier: 4.248A pdb=" N THR H 372 " --> pdb=" O ALA H 363 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA H 363 " --> pdb=" O THR H 372 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2190 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: 5.47 Time building geometry restraints manager: 4.39 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: 5434 1.34 - 1.46: 3788 1.46 - 1.58: 7003 1.58 - 1.70: 0 1.70 - 1.82: 151 Bond restraints: 16376 Sorted by residual: bond pdb=" CG LEU H 217 " pdb=" CD2 LEU H 217 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.74e+00 bond pdb=" CG LEU H 85 " pdb=" CD1 LEU H 85 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.40e+00 bond pdb=" N GLY D 36 " pdb=" CA GLY D 36 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.10e+00 bond pdb=" N GLY E 36 " pdb=" CA GLY E 36 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.01e+00 bond pdb=" CB VAL A 33 " pdb=" CG2 VAL A 33 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.79e+00 ... (remaining 16371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 20597 1.28 - 2.56: 1315 2.56 - 3.85: 234 3.85 - 5.13: 54 5.13 - 6.41: 7 Bond angle restraints: 22207 Sorted by residual: angle pdb=" N ASP H 222 " pdb=" CA ASP H 222 " pdb=" C ASP H 222 " ideal model delta sigma weight residual 112.59 108.30 4.29 1.22e+00 6.72e-01 1.24e+01 angle pdb=" N ILE C 52 " pdb=" CA ILE C 52 " pdb=" C ILE C 52 " ideal model delta sigma weight residual 106.85 111.82 -4.97 1.42e+00 4.96e-01 1.23e+01 angle pdb=" C GLY F 50 " pdb=" N ASP F 51 " pdb=" CA ASP F 51 " ideal model delta sigma weight residual 122.77 118.14 4.63 1.33e+00 5.65e-01 1.21e+01 angle pdb=" N ASP D 248 " pdb=" CA ASP D 248 " pdb=" C ASP D 248 " ideal model delta sigma weight residual 108.46 113.57 -5.11 1.51e+00 4.39e-01 1.15e+01 angle pdb=" N ASP C 42 " pdb=" CA ASP C 42 " pdb=" C ASP C 42 " ideal model delta sigma weight residual 112.54 108.60 3.94 1.22e+00 6.72e-01 1.04e+01 ... (remaining 22202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 9099 17.85 - 35.71: 552 35.71 - 53.56: 126 53.56 - 71.42: 25 71.42 - 89.27: 9 Dihedral angle restraints: 9811 sinusoidal: 3900 harmonic: 5911 Sorted by residual: dihedral pdb=" CA ASN C 65 " pdb=" C ASN C 65 " pdb=" N GLU C 66 " pdb=" CA GLU C 66 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA LEU H 365 " pdb=" C LEU H 365 " pdb=" N ALA H 366 " pdb=" CA ALA H 366 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA LYS H 202 " pdb=" C LYS H 202 " pdb=" N ARG H 203 " pdb=" CA ARG H 203 " ideal model delta harmonic sigma weight residual 180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 9808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1448 0.039 - 0.078: 647 0.078 - 0.117: 268 0.117 - 0.155: 65 0.155 - 0.194: 5 Chirality restraints: 2433 Sorted by residual: chirality pdb=" CB VAL H 236 " pdb=" CA VAL H 236 " pdb=" CG1 VAL H 236 " pdb=" CG2 VAL H 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CB THR E 298 " pdb=" CA THR E 298 " pdb=" OG1 THR E 298 " pdb=" CG2 THR E 298 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CB VAL F 117 " pdb=" CA VAL F 117 " pdb=" CG1 VAL F 117 " pdb=" CG2 VAL F 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 2430 not shown) Planarity restraints: 2930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 109 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO F 110 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO F 110 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 110 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 66 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C GLU C 66 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU C 66 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU C 67 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 2 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 3 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 3 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 3 " -0.024 5.00e-02 4.00e+02 ... (remaining 2927 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2240 2.75 - 3.28: 15933 3.28 - 3.82: 26129 3.82 - 4.36: 31964 4.36 - 4.90: 55336 Nonbonded interactions: 131602 Sorted by model distance: nonbonded pdb=" OG1 THR H 300 " pdb=" O ALA H 354 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR G 9 " pdb=" OD2 ASP H 62 " model vdw 2.248 3.040 nonbonded pdb=" OD1 ASP A 35 " pdb=" NZ LYS F 9 " model vdw 2.250 3.120 nonbonded pdb=" OH TYR C 33 " pdb=" NH2 ARG C 46 " model vdw 2.265 3.120 nonbonded pdb=" O TYR D 416 " pdb=" OG SER D 419 " model vdw 2.281 3.040 ... (remaining 131597 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' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 16.960 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.600 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 0.112 16376 Z= 0.507 Angle : 0.736 6.409 22207 Z= 0.411 Chirality : 0.051 0.194 2433 Planarity : 0.004 0.061 2930 Dihedral : 12.818 89.272 6029 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.53 % Allowed : 2.30 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.16), residues: 2040 helix: -1.24 (0.17), residues: 636 sheet: -0.28 (0.23), residues: 452 loop : -1.30 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 414 HIS 0.007 0.001 HIS G 51 PHE 0.023 0.002 PHE C 152 TYR 0.022 0.003 TYR E 299 ARG 0.010 0.001 ARG C 157 Details of bonding type rmsd hydrogen bonds : bond 0.16598 ( 746) hydrogen bonds : angle 7.91467 ( 2190) covalent geometry : bond 0.01273 (16376) covalent geometry : angle 0.73584 (22207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 257 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.7604 (mmt) cc_final: 0.7390 (mmm) REVERT: E 171 MET cc_start: 0.7669 (mmm) cc_final: 0.7023 (mmt) REVERT: E 180 ARG cc_start: 0.7298 (tpt170) cc_final: 0.6242 (tmt170) REVERT: G 59 ARG cc_start: 0.7694 (ttm170) cc_final: 0.5385 (ptt180) outliers start: 9 outliers final: 3 residues processed: 262 average time/residue: 1.5676 time to fit residues: 445.0438 Evaluate side-chains 164 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 248 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 63 ASN C 116 GLN D 314 ASN D 363 GLN D 402 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN H 223 ASN H 286 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.117946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096320 restraints weight = 28933.423| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.99 r_work: 0.3173 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16376 Z= 0.135 Angle : 0.517 6.664 22207 Z= 0.285 Chirality : 0.044 0.168 2433 Planarity : 0.004 0.058 2930 Dihedral : 4.954 49.986 2262 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.13 % Allowed : 9.40 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2040 helix: 0.53 (0.19), residues: 646 sheet: -0.20 (0.23), residues: 440 loop : -0.48 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 75 HIS 0.002 0.001 HIS F 17 PHE 0.019 0.001 PHE C 152 TYR 0.013 0.001 TYR H 117 ARG 0.006 0.000 ARG D 253 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 746) hydrogen bonds : angle 5.61100 ( 2190) covalent geometry : bond 0.00295 (16376) covalent geometry : angle 0.51671 (22207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 1.926 Fit side-chains REVERT: D 39 GLU cc_start: 0.6173 (pm20) cc_final: 0.4276 (pm20) REVERT: D 48 MET cc_start: 0.8050 (mmt) cc_final: 0.7651 (mmp) REVERT: D 130 MET cc_start: 0.8422 (ttp) cc_final: 0.8119 (ttp) REVERT: D 136 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7257 (mm-30) REVERT: D 248 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7747 (p0) REVERT: D 259 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7219 (mt-10) REVERT: D 283 ARG cc_start: 0.8107 (ttp-170) cc_final: 0.7606 (ttm170) REVERT: E 171 MET cc_start: 0.7237 (mmm) cc_final: 0.6683 (mpt) REVERT: E 178 MET cc_start: 0.1338 (OUTLIER) cc_final: -0.0059 (tpt) REVERT: E 180 ARG cc_start: 0.7149 (tpt170) cc_final: 0.5462 (tmt170) REVERT: E 400 LYS cc_start: 0.8663 (mttp) cc_final: 0.8368 (mtpp) REVERT: E 461 MET cc_start: 0.7883 (mmt) cc_final: 0.7591 (mmt) REVERT: E 481 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: G 68 GLU cc_start: 0.4461 (OUTLIER) cc_final: 0.3842 (tp30) REVERT: H 32 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.9021 (ptt) REVERT: H 68 GLU cc_start: 0.4911 (OUTLIER) cc_final: 0.3825 (tp30) REVERT: H 290 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6018 (pp20) REVERT: H 322 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7269 (m-30) outliers start: 36 outliers final: 8 residues processed: 215 average time/residue: 1.5238 time to fit residues: 357.5213 Evaluate side-chains 187 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 322 ASP Chi-restraints excluded: chain H residue 329 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 102 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 190 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 196 optimal weight: 0.1980 chunk 164 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 GLN D 353 HIS E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 GLN F 31 GLN G 43 ASN H 56 HIS H 337 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.116253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094244 restraints weight = 28862.078| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.99 r_work: 0.3137 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16376 Z= 0.152 Angle : 0.486 5.176 22207 Z= 0.265 Chirality : 0.043 0.165 2433 Planarity : 0.004 0.057 2930 Dihedral : 4.566 34.586 2258 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.07 % Allowed : 10.64 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2040 helix: 1.06 (0.20), residues: 650 sheet: -0.05 (0.23), residues: 441 loop : -0.25 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 75 HIS 0.003 0.001 HIS F 17 PHE 0.018 0.001 PHE C 152 TYR 0.015 0.001 TYR D 458 ARG 0.006 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 746) hydrogen bonds : angle 5.21918 ( 2190) covalent geometry : bond 0.00344 (16376) covalent geometry : angle 0.48552 (22207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 1.660 Fit side-chains revert: symmetry clash REVERT: D 39 GLU cc_start: 0.6539 (pm20) cc_final: 0.5492 (pm20) REVERT: D 48 MET cc_start: 0.8086 (mmt) cc_final: 0.7715 (mmp) REVERT: D 130 MET cc_start: 0.8449 (ttp) cc_final: 0.8101 (ttp) REVERT: D 136 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7333 (mm-30) REVERT: D 180 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6980 (ttt180) REVERT: D 189 MET cc_start: 0.9245 (mmm) cc_final: 0.8926 (mmm) REVERT: D 243 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8305 (mm-40) REVERT: D 259 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: E 159 ILE cc_start: 0.8674 (tp) cc_final: 0.8402 (mp) REVERT: E 171 MET cc_start: 0.7258 (mmm) cc_final: 0.6715 (mpt) REVERT: E 180 ARG cc_start: 0.7127 (tpt170) cc_final: 0.5270 (tmt170) REVERT: E 481 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: G 68 GLU cc_start: 0.4213 (OUTLIER) cc_final: 0.3628 (tp30) REVERT: H 68 GLU cc_start: 0.5025 (OUTLIER) cc_final: 0.3797 (tp30) REVERT: H 290 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6056 (pp20) REVERT: H 307 CYS cc_start: 0.6494 (OUTLIER) cc_final: 0.5977 (p) outliers start: 52 outliers final: 16 residues processed: 224 average time/residue: 1.3264 time to fit residues: 326.6701 Evaluate side-chains 197 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 173 GLU Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 329 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 143 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN D 179 GLN E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.112408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.090235 restraints weight = 29351.086| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.93 r_work: 0.3070 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 16376 Z= 0.300 Angle : 0.585 6.572 22207 Z= 0.316 Chirality : 0.047 0.188 2433 Planarity : 0.004 0.058 2930 Dihedral : 4.855 24.408 2256 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.20 % Allowed : 11.11 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.18), residues: 2040 helix: 0.98 (0.20), residues: 642 sheet: -0.22 (0.25), residues: 407 loop : -0.26 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 249 HIS 0.003 0.001 HIS G 51 PHE 0.022 0.002 PHE C 152 TYR 0.020 0.002 TYR E 299 ARG 0.007 0.001 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 746) hydrogen bonds : angle 5.42512 ( 2190) covalent geometry : bond 0.00702 (16376) covalent geometry : angle 0.58492 (22207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 176 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.8127 (mmt) cc_final: 0.7788 (mmp) REVERT: D 136 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7372 (mm-30) REVERT: D 180 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.7021 (ttt180) REVERT: D 188 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: D 259 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: D 479 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7143 (pt) REVERT: E 171 MET cc_start: 0.7393 (mmm) cc_final: 0.6844 (mpt) REVERT: E 178 MET cc_start: 0.1047 (OUTLIER) cc_final: -0.0626 (tpt) REVERT: E 180 ARG cc_start: 0.7269 (tpt170) cc_final: 0.5573 (tmt170) REVERT: E 481 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: F 68 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9025 (mm) REVERT: G 68 GLU cc_start: 0.4233 (OUTLIER) cc_final: 0.3434 (mp0) REVERT: G 153 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8073 (pt) REVERT: G 173 GLU cc_start: 0.8515 (pm20) cc_final: 0.8081 (tp30) REVERT: G 219 MET cc_start: 0.9114 (tmt) cc_final: 0.8905 (tmt) REVERT: H 68 GLU cc_start: 0.4923 (OUTLIER) cc_final: 0.2981 (tp30) REVERT: H 307 CYS cc_start: 0.6740 (OUTLIER) cc_final: 0.5928 (p) outliers start: 71 outliers final: 22 residues processed: 214 average time/residue: 1.4354 time to fit residues: 336.2929 Evaluate side-chains 197 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 173 GLU Chi-restraints excluded: chain H residue 202 LYS Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 364 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 135 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 HIS D 243 GLN E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 ASN F 31 GLN F 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.114284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.092044 restraints weight = 29541.221| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.00 r_work: 0.3106 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16376 Z= 0.164 Angle : 0.493 7.225 22207 Z= 0.269 Chirality : 0.043 0.165 2433 Planarity : 0.004 0.058 2930 Dihedral : 4.512 21.440 2256 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.07 % Allowed : 12.88 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.18), residues: 2040 helix: 1.21 (0.20), residues: 642 sheet: -0.29 (0.24), residues: 403 loop : -0.16 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 471 HIS 0.003 0.001 HIS F 17 PHE 0.017 0.001 PHE C 152 TYR 0.014 0.001 TYR E 299 ARG 0.005 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 746) hydrogen bonds : angle 5.12447 ( 2190) covalent geometry : bond 0.00372 (16376) covalent geometry : angle 0.49277 (22207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 1.865 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8732 (mmt) REVERT: D 48 MET cc_start: 0.8108 (mmt) cc_final: 0.7707 (mmp) REVERT: D 178 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7224 (tpt) REVERT: D 180 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6910 (ttt180) REVERT: D 188 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: D 243 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8305 (mm110) REVERT: D 259 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: D 347 ASP cc_start: 0.8015 (t0) cc_final: 0.7536 (p0) REVERT: D 479 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7127 (pt) REVERT: E 159 ILE cc_start: 0.8672 (tp) cc_final: 0.8440 (mp) REVERT: E 171 MET cc_start: 0.7271 (mmm) cc_final: 0.6715 (mpt) REVERT: E 180 ARG cc_start: 0.7168 (tpt170) cc_final: 0.5287 (tmt170) REVERT: E 241 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: E 481 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: F 68 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.8974 (mm) REVERT: G 68 GLU cc_start: 0.4147 (OUTLIER) cc_final: 0.3410 (mp0) REVERT: G 173 GLU cc_start: 0.8469 (pm20) cc_final: 0.8030 (tp30) REVERT: H 68 GLU cc_start: 0.5054 (OUTLIER) cc_final: 0.3249 (tp30) REVERT: H 290 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6048 (pp20) REVERT: H 307 CYS cc_start: 0.6692 (OUTLIER) cc_final: 0.5981 (p) outliers start: 52 outliers final: 17 residues processed: 211 average time/residue: 1.5225 time to fit residues: 350.4527 Evaluate side-chains 203 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 350 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 131 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 ASN E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN G 43 ASN G 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.116103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094024 restraints weight = 29084.320| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.03 r_work: 0.3143 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16376 Z= 0.115 Angle : 0.457 7.083 22207 Z= 0.249 Chirality : 0.042 0.167 2433 Planarity : 0.003 0.054 2930 Dihedral : 4.196 19.283 2256 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.66 % Allowed : 13.77 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2040 helix: 1.50 (0.20), residues: 644 sheet: -0.40 (0.23), residues: 437 loop : -0.00 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 249 HIS 0.003 0.000 HIS F 17 PHE 0.015 0.001 PHE C 152 TYR 0.017 0.001 TYR D 242 ARG 0.008 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 746) hydrogen bonds : angle 4.88019 ( 2190) covalent geometry : bond 0.00251 (16376) covalent geometry : angle 0.45724 (22207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.701 Fit side-chains REVERT: A 15 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7891 (mptt) REVERT: D 48 MET cc_start: 0.8056 (mmt) cc_final: 0.7684 (mmp) REVERT: D 178 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.7142 (mmm) REVERT: D 188 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: D 202 MET cc_start: 0.8511 (mtt) cc_final: 0.8158 (mtp) REVERT: D 216 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6947 (mtm) REVERT: D 243 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8279 (mm-40) REVERT: D 259 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: D 347 ASP cc_start: 0.7897 (t0) cc_final: 0.7439 (p0) REVERT: D 479 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7102 (pt) REVERT: E 171 MET cc_start: 0.7224 (mmm) cc_final: 0.6612 (mpt) REVERT: E 180 ARG cc_start: 0.7102 (tpt170) cc_final: 0.5167 (tmt170) REVERT: E 236 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: E 241 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: E 249 TRP cc_start: 0.5400 (t60) cc_final: 0.5014 (p-90) REVERT: E 481 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: F 31 GLN cc_start: 0.8453 (mt0) cc_final: 0.8217 (mt0) REVERT: F 68 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.8919 (mm) REVERT: G 68 GLU cc_start: 0.4331 (OUTLIER) cc_final: 0.3704 (mt-10) REVERT: G 173 GLU cc_start: 0.8460 (pm20) cc_final: 0.8078 (tp30) REVERT: G 261 MET cc_start: 0.8605 (mtp) cc_final: 0.8403 (mtp) REVERT: H 68 GLU cc_start: 0.4910 (OUTLIER) cc_final: 0.3242 (tp30) REVERT: H 307 CYS cc_start: 0.6536 (OUTLIER) cc_final: 0.5935 (p) outliers start: 45 outliers final: 17 residues processed: 215 average time/residue: 1.3848 time to fit residues: 328.4199 Evaluate side-chains 203 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 350 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 22 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 155 optimal weight: 0.0040 chunk 20 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 GLN E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.093933 restraints weight = 29330.200| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.90 r_work: 0.3137 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16376 Z= 0.143 Angle : 0.475 5.852 22207 Z= 0.257 Chirality : 0.042 0.167 2433 Planarity : 0.003 0.052 2930 Dihedral : 4.177 20.237 2256 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.13 % Allowed : 13.83 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2040 helix: 1.55 (0.20), residues: 644 sheet: -0.28 (0.22), residues: 479 loop : 0.00 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 471 HIS 0.003 0.001 HIS F 17 PHE 0.025 0.001 PHE D 247 TYR 0.012 0.001 TYR E 299 ARG 0.008 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 746) hydrogen bonds : angle 4.88359 ( 2190) covalent geometry : bond 0.00324 (16376) covalent geometry : angle 0.47476 (22207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 180 time to evaluate : 1.819 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7868 (mptt) REVERT: C 146 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8218 (mp) REVERT: D 48 MET cc_start: 0.8082 (mmt) cc_final: 0.7711 (mmp) REVERT: D 178 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7177 (mmm) REVERT: D 188 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: D 202 MET cc_start: 0.8507 (mtt) cc_final: 0.8166 (mtp) REVERT: D 216 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6988 (mtm) REVERT: D 243 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8285 (mm110) REVERT: D 259 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: D 347 ASP cc_start: 0.7867 (t0) cc_final: 0.7464 (p0) REVERT: D 479 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7109 (pt) REVERT: D 500 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.6059 (mt-10) REVERT: E 160 MET cc_start: 0.8517 (mtm) cc_final: 0.8282 (mtp) REVERT: E 171 MET cc_start: 0.7289 (mmm) cc_final: 0.6700 (mpt) REVERT: E 180 ARG cc_start: 0.7119 (tpt170) cc_final: 0.5209 (tmt170) REVERT: E 241 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: E 249 TRP cc_start: 0.5502 (t60) cc_final: 0.4977 (p-90) REVERT: E 400 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8318 (mtpp) REVERT: E 481 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: F 68 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8949 (mm) REVERT: G 68 GLU cc_start: 0.4380 (OUTLIER) cc_final: 0.3690 (mt-10) REVERT: G 173 GLU cc_start: 0.8466 (pm20) cc_final: 0.8094 (tp30) REVERT: H 68 GLU cc_start: 0.4752 (OUTLIER) cc_final: 0.2989 (tp30) REVERT: H 137 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8694 (ptp) REVERT: H 241 ASP cc_start: 0.8515 (t70) cc_final: 0.8314 (t0) REVERT: H 307 CYS cc_start: 0.6656 (OUTLIER) cc_final: 0.6010 (p) outliers start: 53 outliers final: 20 residues processed: 213 average time/residue: 1.3957 time to fit residues: 326.2202 Evaluate side-chains 208 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 350 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 55 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 162 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.116894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095044 restraints weight = 29148.613| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.01 r_work: 0.3158 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16376 Z= 0.110 Angle : 0.464 10.202 22207 Z= 0.251 Chirality : 0.041 0.176 2433 Planarity : 0.003 0.048 2930 Dihedral : 4.034 19.622 2256 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.42 % Allowed : 15.01 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2040 helix: 1.67 (0.20), residues: 644 sheet: -0.27 (0.22), residues: 484 loop : 0.06 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 471 HIS 0.003 0.001 HIS F 17 PHE 0.026 0.001 PHE D 247 TYR 0.021 0.001 TYR D 242 ARG 0.009 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 746) hydrogen bonds : angle 4.77413 ( 2190) covalent geometry : bond 0.00244 (16376) covalent geometry : angle 0.46368 (22207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 1.735 Fit side-chains REVERT: A 15 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7862 (mptt) REVERT: D 48 MET cc_start: 0.8047 (mmt) cc_final: 0.7630 (mmp) REVERT: D 178 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7149 (mmm) REVERT: D 188 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: D 202 MET cc_start: 0.8509 (mtt) cc_final: 0.8168 (mtp) REVERT: D 216 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6901 (mtm) REVERT: D 259 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: D 347 ASP cc_start: 0.7842 (t0) cc_final: 0.7384 (p0) REVERT: D 500 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5908 (mt-10) REVERT: E 160 MET cc_start: 0.8500 (mtm) cc_final: 0.8249 (mtp) REVERT: E 171 MET cc_start: 0.7187 (mmm) cc_final: 0.6631 (mpt) REVERT: E 178 MET cc_start: 0.1044 (OUTLIER) cc_final: -0.0750 (tpt) REVERT: E 180 ARG cc_start: 0.7053 (tpt170) cc_final: 0.5132 (tmt170) REVERT: E 241 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: E 249 TRP cc_start: 0.5369 (t60) cc_final: 0.4865 (p-90) REVERT: E 400 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8271 (mtpp) REVERT: E 481 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: F 68 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8935 (mm) REVERT: G 68 GLU cc_start: 0.4361 (OUTLIER) cc_final: 0.3779 (mt-10) REVERT: G 173 GLU cc_start: 0.8461 (pm20) cc_final: 0.8080 (tp30) REVERT: H 68 GLU cc_start: 0.4609 (OUTLIER) cc_final: 0.2951 (tp30) REVERT: H 307 CYS cc_start: 0.6580 (OUTLIER) cc_final: 0.5993 (p) outliers start: 41 outliers final: 18 residues processed: 207 average time/residue: 1.3837 time to fit residues: 313.9855 Evaluate side-chains 204 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 350 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 121 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 166 ASN E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.092926 restraints weight = 29223.912| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.86 r_work: 0.3123 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16376 Z= 0.185 Angle : 0.517 10.996 22207 Z= 0.277 Chirality : 0.043 0.175 2433 Planarity : 0.004 0.051 2930 Dihedral : 4.266 21.229 2256 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.25 % Allowed : 14.72 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2040 helix: 1.55 (0.20), residues: 642 sheet: -0.27 (0.23), residues: 441 loop : -0.03 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 471 HIS 0.003 0.001 HIS E 90 PHE 0.029 0.001 PHE D 247 TYR 0.015 0.001 TYR E 299 ARG 0.009 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 746) hydrogen bonds : angle 4.95396 ( 2190) covalent geometry : bond 0.00425 (16376) covalent geometry : angle 0.51661 (22207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 174 time to evaluate : 1.836 Fit side-chains REVERT: A 15 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7872 (mptt) REVERT: D 48 MET cc_start: 0.8094 (mmt) cc_final: 0.7726 (mmp) REVERT: D 178 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7170 (mmm) REVERT: D 188 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: D 202 MET cc_start: 0.8513 (mtt) cc_final: 0.8172 (mtp) REVERT: D 216 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6996 (mtm) REVERT: D 259 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: D 347 ASP cc_start: 0.8002 (t0) cc_final: 0.7552 (p0) REVERT: D 479 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7208 (pt) REVERT: D 500 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5986 (mt-10) REVERT: E 160 MET cc_start: 0.8565 (mtm) cc_final: 0.8332 (mtp) REVERT: E 171 MET cc_start: 0.7298 (mmm) cc_final: 0.6782 (mpt) REVERT: E 178 MET cc_start: 0.1123 (OUTLIER) cc_final: -0.0714 (tpt) REVERT: E 180 ARG cc_start: 0.7153 (tpt170) cc_final: 0.5268 (tmt170) REVERT: E 241 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: E 249 TRP cc_start: 0.5541 (t60) cc_final: 0.5006 (p-90) REVERT: E 481 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: F 68 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8958 (mm) REVERT: G 68 GLU cc_start: 0.4332 (OUTLIER) cc_final: 0.3557 (mt-10) REVERT: G 173 GLU cc_start: 0.8394 (pm20) cc_final: 0.8144 (tp30) REVERT: H 68 GLU cc_start: 0.4902 (OUTLIER) cc_final: 0.2904 (tp30) REVERT: H 112 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7945 (ttp) REVERT: H 290 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6466 (pp20) REVERT: H 307 CYS cc_start: 0.6631 (OUTLIER) cc_final: 0.5972 (p) REVERT: H 322 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7642 (m-30) outliers start: 55 outliers final: 21 residues processed: 205 average time/residue: 1.4418 time to fit residues: 325.0721 Evaluate side-chains 206 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 322 ASP Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 350 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 29 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 2 optimal weight: 0.0070 chunk 1 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 171 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.117678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.095843 restraints weight = 29423.571| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.02 r_work: 0.3173 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16376 Z= 0.102 Angle : 0.465 10.798 22207 Z= 0.251 Chirality : 0.041 0.194 2433 Planarity : 0.003 0.046 2930 Dihedral : 3.975 19.910 2256 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.25 % Allowed : 15.72 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2040 helix: 1.71 (0.20), residues: 640 sheet: -0.27 (0.22), residues: 477 loop : 0.08 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 471 HIS 0.003 0.000 HIS F 17 PHE 0.016 0.001 PHE D 510 TYR 0.008 0.001 TYR H 117 ARG 0.009 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 746) hydrogen bonds : angle 4.71030 ( 2190) covalent geometry : bond 0.00221 (16376) covalent geometry : angle 0.46546 (22207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 1.830 Fit side-chains REVERT: B 35 ASP cc_start: 0.8600 (t70) cc_final: 0.8381 (t70) REVERT: B 64 SER cc_start: 0.8364 (t) cc_final: 0.7949 (p) REVERT: C 161 LYS cc_start: 0.9203 (tttt) cc_final: 0.8895 (ttpp) REVERT: D 48 MET cc_start: 0.8052 (mmt) cc_final: 0.7671 (mmp) REVERT: D 178 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.7157 (mmm) REVERT: D 188 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: D 202 MET cc_start: 0.8532 (mtt) cc_final: 0.8184 (mtp) REVERT: D 216 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6896 (mtm) REVERT: D 259 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: D 342 LYS cc_start: 0.6794 (mmpt) cc_final: 0.6542 (mptt) REVERT: D 347 ASP cc_start: 0.7821 (t0) cc_final: 0.7362 (p0) REVERT: D 410 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6985 (ttp) REVERT: D 500 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5933 (mt-10) REVERT: E 160 MET cc_start: 0.8467 (mtm) cc_final: 0.8246 (mtp) REVERT: E 171 MET cc_start: 0.7174 (mmm) cc_final: 0.6613 (mpt) REVERT: E 178 MET cc_start: 0.1191 (OUTLIER) cc_final: -0.0660 (tpt) REVERT: E 180 ARG cc_start: 0.7026 (tpt170) cc_final: 0.5034 (tmt170) REVERT: E 241 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: E 481 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: F 68 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8898 (mm) REVERT: G 68 GLU cc_start: 0.4378 (OUTLIER) cc_final: 0.3727 (mt-10) REVERT: G 173 GLU cc_start: 0.8440 (pm20) cc_final: 0.8233 (mp0) REVERT: H 290 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6372 (pp20) REVERT: H 307 CYS cc_start: 0.6588 (OUTLIER) cc_final: 0.6085 (p) outliers start: 38 outliers final: 16 residues processed: 209 average time/residue: 1.4179 time to fit residues: 326.2073 Evaluate side-chains 206 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 350 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 15 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 81 optimal weight: 0.0270 chunk 82 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 192 optimal weight: 0.0670 chunk 152 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** 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 = 0.3604 r_free = 0.3604 target = 0.115692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093846 restraints weight = 29102.647| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.91 r_work: 0.3141 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16376 Z= 0.157 Angle : 0.507 10.063 22207 Z= 0.271 Chirality : 0.043 0.253 2433 Planarity : 0.003 0.050 2930 Dihedral : 4.107 21.904 2256 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.13 % Allowed : 15.90 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2040 helix: 1.61 (0.20), residues: 640 sheet: -0.33 (0.22), residues: 481 loop : 0.05 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 249 HIS 0.002 0.001 HIS F 17 PHE 0.019 0.001 PHE C 152 TYR 0.019 0.001 TYR D 458 ARG 0.009 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 746) hydrogen bonds : angle 4.81381 ( 2190) covalent geometry : bond 0.00361 (16376) covalent geometry : angle 0.50709 (22207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14283.06 seconds wall clock time: 251 minutes 40.01 seconds (15100.01 seconds total)