Starting phenix.real_space_refine on Sat Oct 11 16:18:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vhx_43243/10_2025/8vhx_43243.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vhx_43243/10_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_43243/10_2025/8vhx_43243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vhx_43243/10_2025/8vhx_43243.map" model { file = "/net/cci-nas-00/data/ceres_data/8vhx_43243/10_2025/8vhx_43243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vhx_43243/10_2025/8vhx_43243.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.041 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.58, per 1000 atoms: 0.22 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: 1.00 Conformation dependent library (CDL) restraints added in 682.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.62 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: 3.35 Time building geometry restraints manager: 1.38 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: 20.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.520 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.100 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG C 157 TYR 0.022 0.003 TYR E 299 PHE 0.023 0.002 PHE C 152 TRP 0.023 0.002 TRP E 414 HIS 0.007 0.001 HIS G 51 Details of bonding type rmsd covalent geometry : bond 0.01273 (16376) covalent geometry : angle 0.73584 (22207) hydrogen bonds : bond 0.16598 ( 746) hydrogen bonds : angle 7.91467 ( 2190) *********************** 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 : 0.717 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: 0.7738 time to fit residues: 219.5375 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 : 0.607 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 43 ASN H 223 ASN H 286 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.117056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.095327 restraints weight = 28792.727| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.98 r_work: 0.3155 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16376 Z= 0.156 Angle : 0.524 6.818 22207 Z= 0.289 Chirality : 0.044 0.171 2433 Planarity : 0.004 0.059 2930 Dihedral : 4.952 48.279 2262 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.25 % Allowed : 9.46 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.17), residues: 2040 helix: 0.54 (0.19), residues: 650 sheet: -0.12 (0.23), residues: 440 loop : -0.52 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 253 TYR 0.013 0.001 TYR H 117 PHE 0.019 0.001 PHE C 152 TRP 0.014 0.001 TRP C 75 HIS 0.002 0.001 HIS F 17 Details of bonding type rmsd covalent geometry : bond 0.00338 (16376) covalent geometry : angle 0.52356 (22207) hydrogen bonds : bond 0.04350 ( 746) hydrogen bonds : angle 5.57481 ( 2190) *********************** 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 237 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.633 Fit side-chains REVERT: D 39 GLU cc_start: 0.6263 (pm20) cc_final: 0.4378 (pm20) REVERT: D 48 MET cc_start: 0.8056 (mmt) cc_final: 0.7703 (mmp) REVERT: D 136 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7224 (mm-30) REVERT: D 189 MET cc_start: 0.9239 (mmm) cc_final: 0.8948 (mmm) REVERT: D 259 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: E 171 MET cc_start: 0.7257 (mmm) cc_final: 0.6701 (mpt) REVERT: E 180 ARG cc_start: 0.7169 (tpt170) cc_final: 0.5445 (tmt170) REVERT: E 400 LYS cc_start: 0.8671 (mttp) cc_final: 0.8370 (mtpp) REVERT: E 481 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: G 68 GLU cc_start: 0.4454 (OUTLIER) cc_final: 0.3836 (tp30) REVERT: H 32 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.9069 (ptt) REVERT: H 68 GLU cc_start: 0.4999 (OUTLIER) cc_final: 0.3924 (tp30) REVERT: H 112 MET cc_start: 0.8199 (ttt) cc_final: 0.7833 (ttp) REVERT: H 290 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6016 (pp20) REVERT: H 322 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7227 (m-30) outliers start: 38 outliers final: 9 residues processed: 221 average time/residue: 0.7401 time to fit residues: 178.0355 Evaluate side-chains 186 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 254 MET 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 G residue 68 GLU Chi-restraints excluded: chain G residue 204 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 210 SER Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 322 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 114 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 0.0970 chunk 95 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 51 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 363 GLN F 31 GLN F 59 ASN G 43 ASN H 43 ASN H 337 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097308 restraints weight = 29259.675| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.01 r_work: 0.3195 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16376 Z= 0.100 Angle : 0.448 5.324 22207 Z= 0.247 Chirality : 0.042 0.169 2433 Planarity : 0.003 0.057 2930 Dihedral : 4.249 19.893 2256 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.54 % Allowed : 10.82 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.18), residues: 2040 helix: 1.22 (0.20), residues: 650 sheet: 0.02 (0.23), residues: 437 loop : -0.16 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 31 TYR 0.009 0.001 TYR H 117 PHE 0.015 0.001 PHE C 151 TRP 0.010 0.001 TRP C 75 HIS 0.003 0.000 HIS F 17 Details of bonding type rmsd covalent geometry : bond 0.00208 (16376) covalent geometry : angle 0.44843 (22207) hydrogen bonds : bond 0.03768 ( 746) hydrogen bonds : angle 5.03772 ( 2190) *********************** 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 248 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.671 Fit side-chains REVERT: A 15 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7834 (mptt) REVERT: A 31 ARG cc_start: 0.8369 (ttt-90) cc_final: 0.8094 (ttm110) REVERT: B 64 SER cc_start: 0.8365 (t) cc_final: 0.7942 (p) REVERT: D 39 GLU cc_start: 0.6322 (pm20) cc_final: 0.5097 (pm20) REVERT: D 48 MET cc_start: 0.8063 (mmt) cc_final: 0.7662 (mmp) REVERT: D 136 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7330 (mm-30) REVERT: D 202 MET cc_start: 0.8517 (mtt) cc_final: 0.8158 (mtp) REVERT: D 248 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7814 (p0) REVERT: D 259 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7265 (mt-10) REVERT: D 304 GLU cc_start: 0.4937 (tp30) cc_final: 0.4695 (tt0) REVERT: E 144 MET cc_start: 0.8415 (mmt) cc_final: 0.8082 (mmt) REVERT: E 171 MET cc_start: 0.7224 (mmm) cc_final: 0.6692 (mpt) REVERT: E 178 MET cc_start: 0.1159 (OUTLIER) cc_final: -0.0165 (tpt) REVERT: E 180 ARG cc_start: 0.7044 (tpt170) cc_final: 0.5056 (tmt170) REVERT: F 31 GLN cc_start: 0.8359 (mt0) cc_final: 0.8112 (mt0) REVERT: G 68 GLU cc_start: 0.4403 (OUTLIER) cc_final: 0.3886 (mt-10) REVERT: G 261 MET cc_start: 0.8588 (mtp) cc_final: 0.8367 (mtp) REVERT: H 68 GLU cc_start: 0.4897 (OUTLIER) cc_final: 0.3786 (tp30) REVERT: H 290 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6086 (pp20) REVERT: H 307 CYS cc_start: 0.6345 (m) cc_final: 0.5784 (p) outliers start: 43 outliers final: 13 residues processed: 230 average time/residue: 0.7055 time to fit residues: 178.2299 Evaluate side-chains 195 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 D residue 216 MET Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 342 LYS 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 F residue 36 GLU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR 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 284 THR Chi-restraints excluded: chain H residue 290 GLU 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 170 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 152 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 GLN D 353 HIS E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN H 43 ASN H 56 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.091748 restraints weight = 29458.461| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.87 r_work: 0.3102 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 16376 Z= 0.258 Angle : 0.550 5.807 22207 Z= 0.298 Chirality : 0.045 0.171 2433 Planarity : 0.004 0.056 2930 Dihedral : 4.639 22.970 2256 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.08 % Allowed : 11.41 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.18), residues: 2040 helix: 1.18 (0.20), residues: 642 sheet: -0.10 (0.24), residues: 413 loop : -0.18 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 31 TYR 0.020 0.002 TYR E 299 PHE 0.023 0.002 PHE C 152 TRP 0.012 0.002 TRP E 471 HIS 0.005 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00600 (16376) covalent geometry : angle 0.55042 (22207) hydrogen bonds : bond 0.04384 ( 746) hydrogen bonds : angle 5.28927 ( 2190) *********************** 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: 69 poor density : 178 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: D 39 GLU cc_start: 0.6440 (pm20) cc_final: 0.5709 (pm20) REVERT: D 48 MET cc_start: 0.8104 (mmt) cc_final: 0.7744 (mmp) REVERT: D 136 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7329 (mm-30) REVERT: D 180 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.7035 (ttt180) REVERT: D 188 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8036 (tp-100) REVERT: D 259 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: D 479 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7167 (pt) REVERT: E 144 MET cc_start: 0.8357 (mmt) cc_final: 0.8087 (mmt) REVERT: E 171 MET cc_start: 0.7475 (mmm) cc_final: 0.6918 (mpt) REVERT: E 180 ARG cc_start: 0.7258 (tpt170) cc_final: 0.5373 (tmt170) REVERT: E 249 TRP cc_start: 0.5830 (t60) cc_final: 0.5486 (t60) REVERT: E 481 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: F 68 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.8989 (mm) REVERT: G 68 GLU cc_start: 0.4327 (OUTLIER) cc_final: 0.3550 (tp30) REVERT: G 173 GLU cc_start: 0.8442 (pm20) cc_final: 0.8029 (tp30) REVERT: H 68 GLU cc_start: 0.4728 (OUTLIER) cc_final: 0.2976 (tp30) REVERT: H 307 CYS cc_start: 0.6538 (OUTLIER) cc_final: 0.5842 (p) REVERT: H 322 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7514 (m-30) outliers start: 69 outliers final: 23 residues processed: 220 average time/residue: 0.6789 time to fit residues: 163.5995 Evaluate side-chains 202 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 72 MET Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 124 VAL 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 254 MET 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 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 204 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 43 ASN 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 161 VAL Chi-restraints excluded: chain H residue 169 GLU 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 307 CYS Chi-restraints excluded: chain H residue 322 ASP Chi-restraints excluded: chain H residue 329 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 109 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 HIS E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 ASN F 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.115707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093493 restraints weight = 29387.703| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.04 r_work: 0.3135 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16376 Z= 0.131 Angle : 0.464 5.145 22207 Z= 0.254 Chirality : 0.042 0.166 2433 Planarity : 0.003 0.056 2930 Dihedral : 4.333 20.369 2256 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.31 % Allowed : 12.29 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.18), residues: 2040 helix: 1.42 (0.20), residues: 644 sheet: -0.30 (0.23), residues: 443 loop : -0.03 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 31 TYR 0.012 0.001 TYR H 117 PHE 0.017 0.001 PHE C 152 TRP 0.011 0.001 TRP E 471 HIS 0.003 0.001 HIS F 17 Details of bonding type rmsd covalent geometry : bond 0.00291 (16376) covalent geometry : angle 0.46386 (22207) hydrogen bonds : bond 0.03799 ( 746) hydrogen bonds : angle 5.01488 ( 2190) *********************** 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 243 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.706 Fit side-chains REVERT: A 15 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7866 (mptt) REVERT: D 39 GLU cc_start: 0.6339 (pm20) cc_final: 0.5612 (pm20) REVERT: D 48 MET cc_start: 0.8065 (mmt) cc_final: 0.7669 (mmp) REVERT: D 180 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6913 (ttt180) REVERT: D 188 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7997 (tp-100) REVERT: D 202 MET cc_start: 0.8502 (mtt) cc_final: 0.8165 (mtp) REVERT: D 259 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: D 479 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7121 (pt) REVERT: D 500 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.6030 (mt-10) REVERT: E 171 MET cc_start: 0.7274 (mmm) cc_final: 0.6742 (mpt) REVERT: E 178 MET cc_start: 0.0939 (OUTLIER) cc_final: -0.0772 (tpt) REVERT: E 180 ARG cc_start: 0.7140 (tpt170) cc_final: 0.5197 (tmt170) REVERT: E 400 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8363 (mtpp) REVERT: E 481 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: F 68 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8940 (mm) REVERT: G 68 GLU cc_start: 0.4133 (OUTLIER) cc_final: 0.3541 (mt-10) REVERT: G 173 GLU cc_start: 0.8453 (pm20) cc_final: 0.8002 (tp30) REVERT: G 202 LYS cc_start: 0.8154 (tmtt) cc_final: 0.7867 (tmtm) REVERT: H 68 GLU cc_start: 0.4692 (OUTLIER) cc_final: 0.3144 (tp30) REVERT: H 290 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6055 (pp20) REVERT: H 307 CYS cc_start: 0.6510 (OUTLIER) cc_final: 0.5748 (p) outliers start: 56 outliers final: 18 residues processed: 218 average time/residue: 0.7161 time to fit residues: 170.6741 Evaluate side-chains 207 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 178 MET Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 342 LYS 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 178 MET 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 32 MET 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 G residue 205 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 173 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 48 optimal weight: 0.4980 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 0.0050 chunk 102 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- 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** F 31 GLN G 43 ASN G 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096175 restraints weight = 29413.086| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.95 r_work: 0.3175 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16376 Z= 0.102 Angle : 0.441 6.728 22207 Z= 0.241 Chirality : 0.041 0.169 2433 Planarity : 0.003 0.054 2930 Dihedral : 4.039 18.888 2256 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.66 % Allowed : 13.53 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.18), residues: 2040 helix: 1.66 (0.20), residues: 644 sheet: -0.14 (0.22), residues: 474 loop : 0.06 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 31 TYR 0.009 0.001 TYR D 458 PHE 0.014 0.001 PHE C 151 TRP 0.014 0.001 TRP E 249 HIS 0.003 0.000 HIS F 17 Details of bonding type rmsd covalent geometry : bond 0.00223 (16376) covalent geometry : angle 0.44086 (22207) hydrogen bonds : bond 0.03520 ( 746) hydrogen bonds : angle 4.78475 ( 2190) *********************** 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 229 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.8013 (mptt) REVERT: D 39 GLU cc_start: 0.6204 (pm20) cc_final: 0.5459 (pm20) REVERT: D 44 ASN cc_start: 0.8760 (p0) cc_final: 0.8515 (p0) REVERT: D 48 MET cc_start: 0.8152 (mmt) cc_final: 0.7781 (mmp) REVERT: D 168 CYS cc_start: 0.6968 (t) cc_final: 0.6651 (m) REVERT: D 178 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7126 (mmm) REVERT: D 188 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: D 202 MET cc_start: 0.8517 (mtt) cc_final: 0.8197 (mtp) REVERT: D 216 MET cc_start: 0.7688 (mtm) cc_final: 0.7281 (mtm) REVERT: D 241 GLU cc_start: 0.8123 (pt0) cc_final: 0.7905 (pt0) REVERT: D 259 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: D 479 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7178 (pt) REVERT: D 500 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6326 (mt-10) REVERT: E 171 MET cc_start: 0.7376 (mmm) cc_final: 0.6797 (mpt) REVERT: E 180 ARG cc_start: 0.7034 (tpt170) cc_final: 0.5061 (tmt170) REVERT: E 236 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: E 247 PHE cc_start: 0.6536 (t80) cc_final: 0.6283 (t80) REVERT: E 481 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: F 68 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8884 (mm) REVERT: G 68 GLU cc_start: 0.4686 (OUTLIER) cc_final: 0.4137 (mt-10) REVERT: G 173 GLU cc_start: 0.8343 (pm20) cc_final: 0.8138 (tp30) REVERT: G 202 LYS cc_start: 0.8138 (tmtt) cc_final: 0.7916 (tmtm) REVERT: H 68 GLU cc_start: 0.4988 (OUTLIER) cc_final: 0.3337 (tp30) REVERT: H 290 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6529 (pp20) REVERT: H 307 CYS cc_start: 0.6380 (m) cc_final: 0.5752 (p) outliers start: 45 outliers final: 17 residues processed: 211 average time/residue: 0.7090 time to fit residues: 163.9680 Evaluate side-chains 201 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 178 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 342 LYS 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 236 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 148 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 205 LEU 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 210 SER Chi-restraints excluded: chain H residue 290 GLU 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 105 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 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 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 = 0.114464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092842 restraints weight = 29131.319| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.87 r_work: 0.3121 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16376 Z= 0.201 Angle : 0.502 5.286 22207 Z= 0.271 Chirality : 0.043 0.165 2433 Planarity : 0.004 0.053 2930 Dihedral : 4.310 21.135 2256 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.13 % Allowed : 14.18 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 2040 helix: 1.48 (0.20), residues: 644 sheet: -0.22 (0.22), residues: 479 loop : 0.03 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 31 TYR 0.016 0.001 TYR E 299 PHE 0.021 0.001 PHE C 152 TRP 0.011 0.001 TRP E 249 HIS 0.003 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00464 (16376) covalent geometry : angle 0.50224 (22207) hydrogen bonds : bond 0.03969 ( 746) hydrogen bonds : angle 4.98541 ( 2190) *********************** 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 230 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 0.617 Fit side-chains REVERT: A 15 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7920 (mptt) REVERT: D 48 MET cc_start: 0.8094 (mmt) cc_final: 0.7700 (mmp) REVERT: D 168 CYS cc_start: 0.6934 (t) cc_final: 0.6629 (m) REVERT: D 178 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7155 (mmm) REVERT: D 180 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6946 (ttt180) REVERT: D 188 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: D 216 MET cc_start: 0.7572 (mtm) cc_final: 0.7188 (mtm) REVERT: D 241 GLU cc_start: 0.8163 (pt0) cc_final: 0.7894 (pt0) REVERT: D 259 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: D 347 ASP cc_start: 0.7921 (t0) cc_final: 0.7625 (p0) REVERT: D 479 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7158 (pt) REVERT: D 500 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6140 (mt-10) REVERT: E 171 MET cc_start: 0.7271 (mmm) cc_final: 0.6762 (mpt) REVERT: E 180 ARG cc_start: 0.7166 (tpt170) cc_final: 0.5240 (tmt170) REVERT: E 241 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: E 481 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: F 68 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.8952 (mm) REVERT: G 68 GLU cc_start: 0.4472 (OUTLIER) cc_final: 0.3702 (mt-10) REVERT: G 173 GLU cc_start: 0.8432 (pm20) cc_final: 0.8117 (tp30) REVERT: G 202 LYS cc_start: 0.8189 (tmtt) cc_final: 0.7951 (tmtm) REVERT: G 219 MET cc_start: 0.9064 (tmt) cc_final: 0.8811 (tmt) REVERT: H 68 GLU cc_start: 0.5044 (OUTLIER) cc_final: 0.3109 (tp30) REVERT: H 290 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6097 (pp20) REVERT: H 307 CYS cc_start: 0.6497 (OUTLIER) cc_final: 0.5684 (p) outliers start: 53 outliers final: 24 residues processed: 207 average time/residue: 0.7483 time to fit residues: 169.1501 Evaluate side-chains 208 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 180 ARG Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 342 LYS 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 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 32 MET 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 205 LEU Chi-restraints excluded: chain G residue 254 MET 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 161 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 45 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 153 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- 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 211 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.114414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092605 restraints weight = 29337.089| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.91 r_work: 0.3118 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3058 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= 0.183 Angle : 0.494 5.272 22207 Z= 0.268 Chirality : 0.043 0.169 2433 Planarity : 0.004 0.051 2930 Dihedral : 4.327 21.049 2256 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.19 % Allowed : 14.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.18), residues: 2040 helix: 1.45 (0.20), residues: 644 sheet: -0.21 (0.23), residues: 441 loop : -0.03 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 31 TYR 0.016 0.001 TYR E 299 PHE 0.026 0.001 PHE D 247 TRP 0.018 0.001 TRP D 249 HIS 0.003 0.001 HIS F 17 Details of bonding type rmsd covalent geometry : bond 0.00420 (16376) covalent geometry : angle 0.49366 (22207) hydrogen bonds : bond 0.03921 ( 746) hydrogen bonds : angle 4.98688 ( 2190) *********************** 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 231 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 177 time to evaluate : 0.690 Fit side-chains REVERT: A 15 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7875 (mptt) REVERT: B 35 ASP cc_start: 0.8387 (t0) cc_final: 0.8180 (t70) REVERT: C 146 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8234 (mp) REVERT: D 44 ASN cc_start: 0.8837 (p0) cc_final: 0.8604 (p0) REVERT: D 48 MET cc_start: 0.8057 (mmt) cc_final: 0.7650 (mmp) REVERT: D 168 CYS cc_start: 0.6939 (t) cc_final: 0.6555 (m) REVERT: D 178 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7203 (mmm) REVERT: D 180 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6872 (ttt180) REVERT: D 188 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: D 241 GLU cc_start: 0.8136 (pt0) cc_final: 0.7853 (pt0) REVERT: D 249 TRP cc_start: 0.7522 (t60) cc_final: 0.7297 (t60) REVERT: D 259 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: D 347 ASP cc_start: 0.7992 (t0) cc_final: 0.7611 (p0) REVERT: D 479 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7124 (pt) REVERT: D 500 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5953 (mt-10) REVERT: E 171 MET cc_start: 0.7245 (mmm) cc_final: 0.6723 (mpt) REVERT: E 180 ARG cc_start: 0.7160 (tpt170) cc_final: 0.5237 (tmt170) REVERT: E 241 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: E 481 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: F 68 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.8953 (mm) REVERT: G 68 GLU cc_start: 0.4121 (OUTLIER) cc_final: 0.3394 (mt-10) REVERT: G 173 GLU cc_start: 0.8444 (pm20) cc_final: 0.8109 (tp30) REVERT: G 202 LYS cc_start: 0.8255 (tmtt) cc_final: 0.8018 (tmtm) REVERT: G 219 MET cc_start: 0.9099 (tmt) cc_final: 0.8849 (tmt) REVERT: H 68 GLU cc_start: 0.4844 (OUTLIER) cc_final: 0.3023 (tp30) REVERT: H 112 MET cc_start: 0.8314 (ttt) cc_final: 0.7918 (ttp) REVERT: H 290 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6076 (pp20) REVERT: H 307 CYS cc_start: 0.6606 (OUTLIER) cc_final: 0.5692 (p) outliers start: 54 outliers final: 23 residues processed: 210 average time/residue: 0.7364 time to fit residues: 169.0757 Evaluate side-chains 208 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 180 ARG Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 342 LYS 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 481 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain G residue 32 MET 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 205 LEU Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 45 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 167 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 G 43 ASN G 211 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.114991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093417 restraints weight = 29278.075| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.86 r_work: 0.3130 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16376 Z= 0.157 Angle : 0.479 5.409 22207 Z= 0.259 Chirality : 0.043 0.180 2433 Planarity : 0.003 0.051 2930 Dihedral : 4.240 20.699 2256 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.01 % Allowed : 14.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.18), residues: 2040 helix: 1.54 (0.20), residues: 642 sheet: -0.20 (0.24), residues: 438 loop : -0.00 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 31 TYR 0.014 0.001 TYR E 299 PHE 0.019 0.001 PHE D 510 TRP 0.012 0.001 TRP D 249 HIS 0.003 0.001 HIS F 17 Details of bonding type rmsd covalent geometry : bond 0.00357 (16376) covalent geometry : angle 0.47912 (22207) hydrogen bonds : bond 0.03808 ( 746) hydrogen bonds : angle 4.92134 ( 2190) *********************** 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 223 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.691 Fit side-chains REVERT: A 15 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7880 (mptt) REVERT: C 146 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8194 (mp) REVERT: D 44 ASN cc_start: 0.8822 (p0) cc_final: 0.8553 (p0) REVERT: D 48 MET cc_start: 0.8053 (mmt) cc_final: 0.7642 (mmp) REVERT: D 178 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7208 (mmm) REVERT: D 188 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: D 216 MET cc_start: 0.7353 (mtm) cc_final: 0.7038 (mtm) REVERT: D 241 GLU cc_start: 0.8152 (pt0) cc_final: 0.7864 (pt0) REVERT: D 249 TRP cc_start: 0.7484 (t60) cc_final: 0.7239 (t60) REVERT: D 259 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: D 347 ASP cc_start: 0.7962 (t0) cc_final: 0.7589 (p0) REVERT: D 410 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6992 (ttp) REVERT: D 479 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7173 (pt) REVERT: D 500 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5914 (mt-10) REVERT: E 171 MET cc_start: 0.7244 (mmm) cc_final: 0.6725 (mpt) REVERT: E 178 MET cc_start: 0.1119 (OUTLIER) cc_final: -0.0689 (tpt) REVERT: E 180 ARG cc_start: 0.7134 (tpt170) cc_final: 0.5221 (tmt170) REVERT: E 241 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: E 481 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: F 68 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8934 (mm) REVERT: G 68 GLU cc_start: 0.4166 (OUTLIER) cc_final: 0.3478 (mt-10) REVERT: G 219 MET cc_start: 0.9088 (tmt) cc_final: 0.8852 (tmt) REVERT: H 68 GLU cc_start: 0.4872 (OUTLIER) cc_final: 0.3034 (tp30) REVERT: H 241 ASP cc_start: 0.8592 (t70) cc_final: 0.8387 (t0) REVERT: H 290 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6100 (pp20) REVERT: H 307 CYS cc_start: 0.6631 (OUTLIER) cc_final: 0.5733 (p) outliers start: 51 outliers final: 20 residues processed: 205 average time/residue: 0.7168 time to fit residues: 161.2065 Evaluate side-chains 205 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 254 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 205 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 177 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 93 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 G 43 ASN G 211 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.114805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093062 restraints weight = 29156.133| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.89 r_work: 0.3120 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16376 Z= 0.173 Angle : 0.501 6.033 22207 Z= 0.270 Chirality : 0.043 0.203 2433 Planarity : 0.004 0.050 2930 Dihedral : 4.268 21.761 2256 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.42 % Allowed : 15.13 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 2040 helix: 1.52 (0.20), residues: 642 sheet: -0.18 (0.24), residues: 436 loop : -0.05 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 31 TYR 0.015 0.001 TYR E 299 PHE 0.033 0.001 PHE D 247 TRP 0.012 0.001 TRP D 249 HIS 0.003 0.001 HIS F 17 Details of bonding type rmsd covalent geometry : bond 0.00396 (16376) covalent geometry : angle 0.50083 (22207) hydrogen bonds : bond 0.03880 ( 746) hydrogen bonds : angle 4.94486 ( 2190) ********************** 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 211 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.659 Fit side-chains REVERT: A 15 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7891 (mptt) REVERT: C 146 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8220 (mp) REVERT: D 44 ASN cc_start: 0.8823 (p0) cc_final: 0.8553 (p0) REVERT: D 48 MET cc_start: 0.8062 (mmt) cc_final: 0.7655 (mmp) REVERT: D 178 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7211 (mmm) REVERT: D 188 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: D 216 MET cc_start: 0.7302 (mtm) cc_final: 0.6989 (mtm) REVERT: D 259 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: D 347 ASP cc_start: 0.8005 (t0) cc_final: 0.7634 (p0) REVERT: D 410 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.7017 (ttp) REVERT: D 479 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7214 (pt) REVERT: D 500 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5932 (mt-10) REVERT: E 171 MET cc_start: 0.7251 (mmm) cc_final: 0.6727 (mpt) REVERT: E 178 MET cc_start: 0.1083 (OUTLIER) cc_final: -0.0685 (tpt) REVERT: E 180 ARG cc_start: 0.7143 (tpt170) cc_final: 0.5243 (tmt170) REVERT: E 241 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: E 481 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: F 68 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.8950 (mm) REVERT: G 68 GLU cc_start: 0.4150 (OUTLIER) cc_final: 0.3393 (mp0) REVERT: G 173 GLU cc_start: 0.8495 (mp0) cc_final: 0.8252 (tp30) REVERT: G 219 MET cc_start: 0.9098 (tmt) cc_final: 0.8864 (tmt) REVERT: H 68 GLU cc_start: 0.4779 (OUTLIER) cc_final: 0.2853 (tp30) REVERT: H 290 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6081 (pp20) REVERT: H 307 CYS cc_start: 0.6657 (OUTLIER) cc_final: 0.5693 (p) outliers start: 41 outliers final: 22 residues processed: 197 average time/residue: 0.7160 time to fit residues: 154.7142 Evaluate side-chains 203 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 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 254 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 205 LEU Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 177 ILE 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 93 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 162 optimal weight: 0.0770 chunk 65 optimal weight: 3.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.114813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.093195 restraints weight = 29178.554| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.85 r_work: 0.3126 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 16376 Z= 0.181 Angle : 0.724 59.198 22207 Z= 0.423 Chirality : 0.047 0.944 2433 Planarity : 0.004 0.056 2930 Dihedral : 4.314 29.140 2256 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.25 % Allowed : 15.43 % Favored : 82.33 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 2040 helix: 1.53 (0.20), residues: 642 sheet: -0.18 (0.24), residues: 436 loop : -0.05 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 31 TYR 0.015 0.001 TYR E 299 PHE 0.028 0.001 PHE D 247 TRP 0.040 0.001 TRP D 249 HIS 0.003 0.001 HIS F 17 Details of bonding type rmsd covalent geometry : bond 0.00389 (16376) covalent geometry : angle 0.72361 (22207) hydrogen bonds : bond 0.03869 ( 746) hydrogen bonds : angle 4.94642 ( 2190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7430.05 seconds wall clock time: 127 minutes 1.49 seconds (7621.49 seconds total)