Starting phenix.real_space_refine on Sat Jun 14 07:56:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vhx_43243/06_2025/8vhx_43243.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vhx_43243/06_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_43243/06_2025/8vhx_43243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vhx_43243/06_2025/8vhx_43243.map" model { file = "/net/cci-nas-00/data/ceres_data/8vhx_43243/06_2025/8vhx_43243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vhx_43243/06_2025/8vhx_43243.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 10089 2.51 5 N 2788 2.21 5 O 3097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 151 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16055 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "B" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "C" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1316 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 154} Chain: "D" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3789 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 24, 'TRANS': 454} Chain breaks: 1 Chain: "E" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3789 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 24, 'TRANS': 454} Chain breaks: 1 Chain: "F" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "G" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2138 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 266} Chain: "H" Number of atoms: 2788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2788 Classifications: {'peptide': 375} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 363} Time building chain proxies: 12.16, per 1000 atoms: 0.76 Number of scatterers: 16055 At special positions: 0 Unit cell: (103.32, 134.48, 289.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 3097 8.00 N 2788 7.00 C 10089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 2.0 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3782 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 27 sheets defined 35.8% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 2 through 27 Processing helix chain 'A' and resid 47 through 64 Processing helix chain 'A' and resid 66 through 73 removed outlier: 4.387A pdb=" N MET A 72 " --> pdb=" O CYS A 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 47 through 64 Processing helix chain 'B' and resid 66 through 73 removed outlier: 4.099A pdb=" N MET B 72 " --> pdb=" O CYS B 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 17 through 18 No H-bonds generated for 'chain 'C' and resid 17 through 18' Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 65 through 68 Processing helix chain 'C' and resid 91 through 107 removed outlier: 3.980A pdb=" N TYR C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET C 107 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.990A pdb=" N GLY C 127 " --> pdb=" O TYR C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 42 removed outlier: 3.807A pdb=" N GLU D 42 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 80 through 95 Processing helix chain 'D' and resid 115 through 133 removed outlier: 3.532A pdb=" N GLU D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 162 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 235 through 238 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.869A pdb=" N ALA D 274 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 299 removed outlier: 3.513A pdb=" N TYR D 299 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'D' and resid 402 through 424 removed outlier: 3.745A pdb=" N TYR D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 444 Processing helix chain 'D' and resid 455 through 458 Processing helix chain 'D' and resid 459 through 468 Processing helix chain 'D' and resid 483 through 494 Processing helix chain 'D' and resid 498 through 506 Processing helix chain 'D' and resid 509 through 528 Processing helix chain 'E' and resid 57 through 65 Processing helix chain 'E' and resid 66 through 80 Processing helix chain 'E' and resid 80 through 95 Processing helix chain 'E' and resid 106 through 111 Processing helix chain 'E' and resid 116 through 133 removed outlier: 3.570A pdb=" N VAL E 131 " --> pdb=" O ARG E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 162 Processing helix chain 'E' and resid 176 through 180 Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 197 through 201 Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.765A pdb=" N GLN E 237 " --> pdb=" O ASP E 234 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP E 238 " --> pdb=" O LEU E 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 238' Processing helix chain 'E' and resid 270 through 274 Processing helix chain 'E' and resid 275 through 299 removed outlier: 3.733A pdb=" N TYR E 299 " --> pdb=" O VAL E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 317 Processing helix chain 'E' and resid 373 through 388 removed outlier: 3.599A pdb=" N SER E 386 " --> pdb=" O ASN E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 396 Processing helix chain 'E' and resid 402 through 424 Processing helix chain 'E' and resid 424 through 444 Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 459 through 468 removed outlier: 3.765A pdb=" N LEU E 466 " --> pdb=" O LYS E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 494 Processing helix chain 'E' and resid 498 through 506 Processing helix chain 'E' and resid 509 through 528 removed outlier: 3.517A pdb=" N VAL E 513 " --> pdb=" O ASP E 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 21 Processing helix chain 'F' and resid 71 through 78 Processing helix chain 'G' and resid 81 through 89 Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'H' and resid 81 through 89 Processing helix chain 'H' and resid 152 through 156 Processing helix chain 'H' and resid 367 through 369 No H-bonds generated for 'chain 'H' and resid 367 through 369' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 4.743A pdb=" N SER A 29 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU B 42 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL A 33 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG B 40 " --> pdb=" O VAL A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 82 removed outlier: 6.479A pdb=" N GLY B 80 " --> pdb=" O ILE E 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.655A pdb=" N LEU C 160 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.655A pdb=" N LEU C 160 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE C 151 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 140 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 100 through 103 Processing sheet with id=AA7, first strand: chain 'D' and resid 185 through 189 Processing sheet with id=AA8, first strand: chain 'D' and resid 207 through 208 removed outlier: 3.741A pdb=" N GLY D 221 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 301 through 304 Processing sheet with id=AB1, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB2, first strand: chain 'E' and resid 100 through 103 Processing sheet with id=AB3, first strand: chain 'E' and resid 188 through 189 Processing sheet with id=AB4, first strand: chain 'E' and resid 207 through 208 Processing sheet with id=AB5, first strand: chain 'F' and resid 22 through 27 removed outlier: 5.977A pdb=" N VAL F 22 " --> pdb=" O SER F 39 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER F 39 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA F 24 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER F 39 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR F 70 " --> pdb=" O SER F 39 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY F 63 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG F 119 " --> pdb=" O GLY F 63 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU F 65 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL F 114 " --> pdb=" O GLN F 104 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLN F 104 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN F 116 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 31 through 33 removed outlier: 6.604A pdb=" N VAL G 213 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER G 237 " --> pdb=" O VAL G 213 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY G 215 " --> pdb=" O LYS G 235 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS G 235 " --> pdb=" O GLY G 215 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER G 221 " --> pdb=" O LYS G 229 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LYS G 229 " --> pdb=" O SER G 221 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER G 255 " --> pdb=" O ASP G 241 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN G 71 " --> pdb=" O ALA G 260 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL G 65 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU G 47 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA G 69 " --> pdb=" O ASP G 45 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP G 45 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 39 through 41 removed outlier: 4.226A pdb=" N GLU G 39 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN G 71 " --> pdb=" O ALA G 260 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER G 255 " --> pdb=" O ASP G 241 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 92 through 97 Processing sheet with id=AB9, first strand: chain 'G' and resid 101 through 108 removed outlier: 3.579A pdb=" N ASP G 103 " --> pdb=" O TYR G 196 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N TYR G 196 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS G 105 " --> pdb=" O VAL G 194 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 194 " --> pdb=" O LYS G 105 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL G 107 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE G 192 " --> pdb=" O VAL G 107 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASP G 197 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ASN G 134 " --> pdb=" O ASP G 197 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N MET G 137 " --> pdb=" O VAL G 162 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 116 through 118 Processing sheet with id=AC2, first strand: chain 'H' and resid 28 through 33 removed outlier: 4.444A pdb=" N GLY H 30 " --> pdb=" O ARG H 20 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG H 20 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR H 214 " --> pdb=" O PHE H 21 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL H 213 " --> pdb=" O SER H 237 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER H 237 " --> pdb=" O VAL H 213 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY H 215 " --> pdb=" O LYS H 235 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS H 235 " --> pdb=" O GLY H 215 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 221 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS H 229 " --> pdb=" O SER H 221 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER H 255 " --> pdb=" O ASP H 241 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU H 39 " --> pdb=" O THR H 76 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 28 through 33 removed outlier: 4.444A pdb=" N GLY H 30 " --> pdb=" O ARG H 20 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG H 20 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR H 214 " --> pdb=" O PHE H 21 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL H 213 " --> pdb=" O SER H 237 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER H 237 " --> pdb=" O VAL H 213 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY H 215 " --> pdb=" O LYS H 235 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS H 235 " --> pdb=" O GLY H 215 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 221 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS H 229 " --> pdb=" O SER H 221 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN H 228 " --> pdb=" O VAL H 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 45 through 52 removed outlier: 6.087A pdb=" N ASP H 45 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA H 69 " --> pdb=" O ASP H 45 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU H 47 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 92 through 98 removed outlier: 3.788A pdb=" N GLN H 201 " --> pdb=" O GLN H 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 101 through 108 removed outlier: 5.591A pdb=" N THR H 102 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL H 198 " --> pdb=" O THR H 102 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP H 197 " --> pdb=" O ASN H 134 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN H 134 " --> pdb=" O ASP H 197 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 115 through 118 removed outlier: 3.710A pdb=" N ARG H 115 " --> pdb=" O ILE H 179 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 288 through 293 removed outlier: 3.572A pdb=" N THR H 349 " --> pdb=" O CYS H 307 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 297 through 299 removed outlier: 4.248A pdb=" N THR H 372 " --> pdb=" O ALA H 363 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA H 363 " --> pdb=" O THR H 372 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.33 Time building geometry restraints manager: 4.34 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: 9.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.430 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.112 16376 Z= 0.507 Angle : 0.736 6.409 22207 Z= 0.411 Chirality : 0.051 0.194 2433 Planarity : 0.004 0.061 2930 Dihedral : 12.818 89.272 6029 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.53 % Allowed : 2.30 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.16), residues: 2040 helix: -1.24 (0.17), residues: 636 sheet: -0.28 (0.23), residues: 452 loop : -1.30 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 414 HIS 0.007 0.001 HIS G 51 PHE 0.023 0.002 PHE C 152 TYR 0.022 0.003 TYR E 299 ARG 0.010 0.001 ARG C 157 Details of bonding type rmsd hydrogen bonds : bond 0.16598 ( 746) hydrogen bonds : angle 7.91467 ( 2190) covalent geometry : bond 0.01273 (16376) covalent geometry : angle 0.73584 (22207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 257 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.7604 (mmt) cc_final: 0.7390 (mmm) REVERT: E 171 MET cc_start: 0.7669 (mmm) cc_final: 0.7023 (mmt) REVERT: E 180 ARG cc_start: 0.7298 (tpt170) cc_final: 0.6242 (tmt170) REVERT: G 59 ARG cc_start: 0.7694 (ttm170) cc_final: 0.5385 (ptt180) outliers start: 9 outliers final: 3 residues processed: 262 average time/residue: 1.6639 time to fit residues: 471.7567 Evaluate side-chains 164 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 248 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 63 ASN C 116 GLN D 314 ASN D 363 GLN D 402 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN H 223 ASN H 286 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.117946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096320 restraints weight = 28933.426| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.99 r_work: 0.3173 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16376 Z= 0.135 Angle : 0.517 6.664 22207 Z= 0.285 Chirality : 0.044 0.168 2433 Planarity : 0.004 0.058 2930 Dihedral : 4.954 49.986 2262 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.13 % Allowed : 9.40 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2040 helix: 0.53 (0.19), residues: 646 sheet: -0.20 (0.23), residues: 440 loop : -0.48 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 75 HIS 0.002 0.001 HIS F 17 PHE 0.019 0.001 PHE C 152 TYR 0.013 0.001 TYR H 117 ARG 0.006 0.000 ARG D 253 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 746) hydrogen bonds : angle 5.61100 ( 2190) covalent geometry : bond 0.00295 (16376) covalent geometry : angle 0.51671 (22207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 1.745 Fit side-chains REVERT: D 39 GLU cc_start: 0.6173 (pm20) cc_final: 0.4276 (pm20) REVERT: D 48 MET cc_start: 0.8050 (mmt) cc_final: 0.7650 (mmp) REVERT: D 130 MET cc_start: 0.8422 (ttp) cc_final: 0.8118 (ttp) REVERT: D 136 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7258 (mm-30) REVERT: D 248 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7748 (p0) REVERT: D 259 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7219 (mt-10) REVERT: D 283 ARG cc_start: 0.8108 (ttp-170) cc_final: 0.7606 (ttm170) REVERT: E 171 MET cc_start: 0.7238 (mmm) cc_final: 0.6684 (mpt) REVERT: E 178 MET cc_start: 0.1339 (OUTLIER) cc_final: -0.0058 (tpt) REVERT: E 180 ARG cc_start: 0.7150 (tpt170) cc_final: 0.5463 (tmt170) REVERT: E 400 LYS cc_start: 0.8663 (mttp) cc_final: 0.8369 (mtpp) REVERT: E 461 MET cc_start: 0.7883 (mmt) cc_final: 0.7591 (mmt) REVERT: E 481 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: G 68 GLU cc_start: 0.4463 (OUTLIER) cc_final: 0.3844 (tp30) REVERT: H 32 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.9020 (ptt) REVERT: H 68 GLU cc_start: 0.4912 (OUTLIER) cc_final: 0.3827 (tp30) REVERT: H 290 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6019 (pp20) REVERT: H 322 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7269 (m-30) outliers start: 36 outliers final: 8 residues processed: 215 average time/residue: 1.5351 time to fit residues: 360.2241 Evaluate side-chains 187 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 322 ASP Chi-restraints excluded: chain H residue 329 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 102 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 190 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 GLN D 353 HIS E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 GLN F 31 GLN G 43 ASN H 56 HIS H 337 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.115109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.093542 restraints weight = 28936.608| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.84 r_work: 0.3131 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16376 Z= 0.189 Angle : 0.511 5.191 22207 Z= 0.279 Chirality : 0.044 0.165 2433 Planarity : 0.004 0.057 2930 Dihedral : 4.731 37.168 2258 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.31 % Allowed : 10.64 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2040 helix: 0.94 (0.19), residues: 648 sheet: -0.01 (0.24), residues: 411 loop : -0.33 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 249 HIS 0.003 0.001 HIS F 17 PHE 0.019 0.001 PHE C 152 TYR 0.016 0.001 TYR H 117 ARG 0.006 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 746) hydrogen bonds : angle 5.33183 ( 2190) covalent geometry : bond 0.00433 (16376) covalent geometry : angle 0.51148 (22207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 2.368 Fit side-chains revert: symmetry clash REVERT: D 39 GLU cc_start: 0.6586 (pm20) cc_final: 0.5909 (pm20) REVERT: D 48 MET cc_start: 0.8095 (mmt) cc_final: 0.7722 (mmp) REVERT: D 130 MET cc_start: 0.8448 (ttp) cc_final: 0.8107 (ttp) REVERT: D 136 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7265 (mm-30) REVERT: D 180 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6960 (ttt180) REVERT: D 243 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8213 (mm-40) REVERT: D 259 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: E 171 MET cc_start: 0.7271 (mmm) cc_final: 0.6722 (mpt) REVERT: E 180 ARG cc_start: 0.7155 (tpt170) cc_final: 0.5410 (tmt170) REVERT: E 400 LYS cc_start: 0.8581 (mttp) cc_final: 0.8363 (mtpp) REVERT: E 461 MET cc_start: 0.7919 (mmt) cc_final: 0.7685 (mmt) REVERT: E 481 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: G 68 GLU cc_start: 0.4273 (OUTLIER) cc_final: 0.3656 (tp30) REVERT: H 68 GLU cc_start: 0.4963 (OUTLIER) cc_final: 0.3612 (tp30) REVERT: H 307 CYS cc_start: 0.6567 (OUTLIER) cc_final: 0.5819 (p) outliers start: 56 outliers final: 19 residues processed: 220 average time/residue: 1.6348 time to fit residues: 393.9211 Evaluate side-chains 200 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 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 241 ASP Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 329 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 143 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 39 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 GLN 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 = 0.3576 r_free = 0.3576 target = 0.114221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092572 restraints weight = 29191.739| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.86 r_work: 0.3114 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16376 Z= 0.207 Angle : 0.513 5.195 22207 Z= 0.279 Chirality : 0.044 0.166 2433 Planarity : 0.004 0.058 2930 Dihedral : 4.586 22.094 2256 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.49 % Allowed : 11.47 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.18), residues: 2040 helix: 1.02 (0.19), residues: 654 sheet: -0.15 (0.24), residues: 413 loop : -0.29 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 249 HIS 0.003 0.001 HIS F 17 PHE 0.020 0.001 PHE C 152 TYR 0.016 0.001 TYR H 117 ARG 0.007 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 746) hydrogen bonds : angle 5.23940 ( 2190) covalent geometry : bond 0.00476 (16376) covalent geometry : angle 0.51281 (22207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 1.944 Fit side-chains revert: symmetry clash REVERT: D 39 GLU cc_start: 0.6455 (pm20) cc_final: 0.5738 (pm20) REVERT: D 48 MET cc_start: 0.8100 (mmt) cc_final: 0.7737 (mmp) REVERT: D 130 MET cc_start: 0.8477 (ttp) cc_final: 0.8142 (ttp) REVERT: D 136 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7323 (mm-30) REVERT: D 180 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6976 (ttt180) REVERT: D 259 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: D 479 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7172 (pt) REVERT: E 159 ILE cc_start: 0.8742 (tp) cc_final: 0.8481 (mp) REVERT: E 171 MET cc_start: 0.7369 (mmm) cc_final: 0.6823 (mpt) REVERT: E 180 ARG cc_start: 0.7209 (tpt170) cc_final: 0.5406 (tmt170) REVERT: E 481 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: F 68 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9021 (mm) REVERT: G 68 GLU cc_start: 0.4382 (OUTLIER) cc_final: 0.3669 (tp30) REVERT: G 173 GLU cc_start: 0.8433 (pm20) cc_final: 0.8049 (tp30) REVERT: G 219 MET cc_start: 0.9061 (tmt) cc_final: 0.8832 (tmt) REVERT: H 68 GLU cc_start: 0.4722 (OUTLIER) cc_final: 0.3000 (tp30) REVERT: H 290 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6059 (pp20) REVERT: H 307 CYS cc_start: 0.6581 (OUTLIER) cc_final: 0.5925 (p) outliers start: 59 outliers final: 22 residues processed: 217 average time/residue: 1.4607 time to fit residues: 347.8881 Evaluate side-chains 205 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 1.933 ------------------------------------------------------------------------------- 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 118 MET Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 133 GLU 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 169 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 169 GLU 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 364 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 135 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 HIS D 243 GLN E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN F 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092351 restraints weight = 29713.490| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.82 r_work: 0.3117 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16376 Z= 0.193 Angle : 0.504 5.217 22207 Z= 0.274 Chirality : 0.044 0.165 2433 Planarity : 0.004 0.057 2930 Dihedral : 4.511 21.753 2256 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.78 % Allowed : 11.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.18), residues: 2040 helix: 1.22 (0.20), residues: 644 sheet: -0.23 (0.23), residues: 441 loop : -0.18 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 249 HIS 0.003 0.001 HIS F 17 PHE 0.019 0.001 PHE C 152 TYR 0.015 0.001 TYR E 299 ARG 0.007 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 746) hydrogen bonds : angle 5.16474 ( 2190) covalent geometry : bond 0.00444 (16376) covalent geometry : angle 0.50357 (22207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 181 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: D 48 MET cc_start: 0.8077 (mmt) cc_final: 0.7722 (mmp) REVERT: D 180 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6930 (ttt180) REVERT: D 243 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8145 (mm-40) REVERT: D 259 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: D 347 ASP cc_start: 0.7995 (t0) cc_final: 0.7568 (p0) REVERT: D 479 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7124 (pt) REVERT: E 159 ILE cc_start: 0.8696 (tp) cc_final: 0.8439 (mp) REVERT: E 171 MET cc_start: 0.7289 (mmm) cc_final: 0.6735 (mpt) REVERT: E 178 MET cc_start: 0.1026 (OUTLIER) cc_final: -0.0650 (tpt) REVERT: E 180 ARG cc_start: 0.7175 (tpt170) cc_final: 0.5299 (tmt170) REVERT: E 236 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: E 241 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: E 481 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: F 68 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.8990 (mm) REVERT: G 68 GLU cc_start: 0.4178 (OUTLIER) cc_final: 0.3420 (mp0) REVERT: G 139 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7976 (ttpp) REVERT: G 173 GLU cc_start: 0.8440 (pm20) cc_final: 0.8011 (tp30) REVERT: G 219 MET cc_start: 0.9090 (tmt) cc_final: 0.8875 (tmt) REVERT: H 68 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.3076 (tp30) REVERT: H 290 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.5997 (pp20) REVERT: H 307 CYS cc_start: 0.6712 (OUTLIER) cc_final: 0.5966 (p) outliers start: 64 outliers final: 27 residues processed: 216 average time/residue: 1.6775 time to fit residues: 397.7583 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 : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 241 GLU 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 139 LYS Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 173 GLU Chi-restraints excluded: chain H residue 202 LYS Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 364 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 131 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 GLN E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN G 43 ASN G 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.115822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093733 restraints weight = 29072.263| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.00 r_work: 0.3134 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16376 Z= 0.125 Angle : 0.461 7.178 22207 Z= 0.252 Chirality : 0.042 0.166 2433 Planarity : 0.003 0.055 2930 Dihedral : 4.254 19.741 2256 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.13 % Allowed : 12.88 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2040 helix: 1.44 (0.20), residues: 644 sheet: -0.36 (0.23), residues: 443 loop : -0.06 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 471 HIS 0.003 0.001 HIS F 17 PHE 0.017 0.001 PHE D 510 TYR 0.017 0.001 TYR D 242 ARG 0.008 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 746) hydrogen bonds : angle 4.95189 ( 2190) covalent geometry : bond 0.00278 (16376) covalent geometry : angle 0.46133 (22207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 1.977 Fit side-chains REVERT: A 15 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7875 (mptt) REVERT: D 48 MET cc_start: 0.8077 (mmt) cc_final: 0.7713 (mmp) REVERT: D 178 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7052 (tmm) REVERT: D 216 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6985 (mtm) REVERT: D 243 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8209 (mm-40) REVERT: D 259 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: D 347 ASP cc_start: 0.7939 (t0) cc_final: 0.7461 (p0) REVERT: D 479 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7083 (pt) REVERT: E 171 MET cc_start: 0.7215 (mmm) cc_final: 0.6680 (mpt) REVERT: E 180 ARG cc_start: 0.7123 (tpt170) cc_final: 0.5185 (tmt170) REVERT: E 241 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: E 481 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: F 68 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.8919 (mm) REVERT: G 68 GLU cc_start: 0.4309 (OUTLIER) cc_final: 0.3671 (mt-10) REVERT: G 173 GLU cc_start: 0.8457 (pm20) cc_final: 0.8053 (tp30) REVERT: G 261 MET cc_start: 0.8588 (mtp) cc_final: 0.8356 (mtp) REVERT: H 68 GLU cc_start: 0.4928 (OUTLIER) cc_final: 0.3205 (tp30) REVERT: H 290 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6066 (pp20) REVERT: H 307 CYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6062 (p) outliers start: 53 outliers final: 18 residues processed: 214 average time/residue: 1.6018 time to fit residues: 377.6322 Evaluate side-chains 200 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 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 307 CYS Chi-restraints excluded: chain H residue 329 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 22 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 GLN E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN G 43 ASN G 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.115131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.092904 restraints weight = 29318.017| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.01 r_work: 0.3121 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16376 Z= 0.158 Angle : 0.482 7.418 22207 Z= 0.261 Chirality : 0.042 0.164 2433 Planarity : 0.004 0.055 2930 Dihedral : 4.262 20.031 2256 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.07 % Allowed : 13.48 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2040 helix: 1.50 (0.20), residues: 644 sheet: -0.31 (0.22), residues: 479 loop : -0.05 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 471 HIS 0.003 0.001 HIS E 90 PHE 0.018 0.001 PHE C 152 TYR 0.021 0.001 TYR D 458 ARG 0.008 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 746) hydrogen bonds : angle 4.95733 ( 2190) covalent geometry : bond 0.00360 (16376) covalent geometry : angle 0.48206 (22207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 1.681 Fit side-chains REVERT: A 15 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7887 (mptt) REVERT: D 48 MET cc_start: 0.8070 (mmt) cc_final: 0.7666 (mmp) REVERT: D 168 CYS cc_start: 0.6975 (t) cc_final: 0.6595 (m) REVERT: D 178 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7133 (mmm) REVERT: D 188 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8029 (tp-100) REVERT: D 202 MET cc_start: 0.8501 (mtt) cc_final: 0.8144 (mtp) REVERT: D 216 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7023 (mtm) REVERT: D 243 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8447 (mm110) REVERT: D 259 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: D 347 ASP cc_start: 0.7976 (t0) cc_final: 0.7504 (p0) REVERT: D 479 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7110 (pt) REVERT: E 160 MET cc_start: 0.8511 (ttm) cc_final: 0.8246 (mtp) REVERT: E 171 MET cc_start: 0.7224 (mmm) cc_final: 0.6690 (mpt) REVERT: E 180 ARG cc_start: 0.7141 (tpt170) cc_final: 0.5195 (tmt170) REVERT: E 241 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: E 481 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: F 68 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.8977 (mm) REVERT: G 68 GLU cc_start: 0.4252 (OUTLIER) cc_final: 0.3570 (mt-10) REVERT: G 173 GLU cc_start: 0.8461 (pm20) cc_final: 0.8038 (tp30) REVERT: G 261 MET cc_start: 0.8599 (mtp) cc_final: 0.8363 (mtp) REVERT: H 68 GLU cc_start: 0.4615 (OUTLIER) cc_final: 0.2859 (tp30) REVERT: H 290 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6059 (pp20) REVERT: H 307 CYS cc_start: 0.6749 (OUTLIER) cc_final: 0.5995 (p) outliers start: 52 outliers final: 22 residues processed: 206 average time/residue: 1.4316 time to fit residues: 322.8846 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 : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 173 GLU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 202 LYS Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 307 CYS Chi-restraints excluded: chain H residue 329 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 55 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 51 optimal weight: 0.0370 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.115544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.093911 restraints weight = 29175.732| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.91 r_work: 0.3134 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16376 Z= 0.143 Angle : 0.477 7.841 22207 Z= 0.258 Chirality : 0.042 0.173 2433 Planarity : 0.003 0.054 2930 Dihedral : 4.217 20.279 2256 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.90 % Allowed : 14.48 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2040 helix: 1.55 (0.20), residues: 644 sheet: -0.34 (0.22), residues: 479 loop : -0.04 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 249 HIS 0.003 0.001 HIS F 17 PHE 0.028 0.001 PHE D 247 TYR 0.023 0.001 TYR D 458 ARG 0.010 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 746) hydrogen bonds : angle 4.89733 ( 2190) covalent geometry : bond 0.00324 (16376) covalent geometry : angle 0.47673 (22207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 1.986 Fit side-chains REVERT: D 48 MET cc_start: 0.8190 (mmt) cc_final: 0.7816 (mmp) REVERT: D 171 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7382 (mpt) REVERT: D 178 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7223 (mmm) REVERT: D 202 MET cc_start: 0.8527 (mtt) cc_final: 0.8203 (mtp) REVERT: D 216 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7119 (mtm) REVERT: D 243 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8445 (mm110) REVERT: D 259 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: D 347 ASP cc_start: 0.7914 (t0) cc_final: 0.7633 (p0) REVERT: D 479 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7191 (pt) REVERT: D 500 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6195 (mt-10) REVERT: E 160 MET cc_start: 0.8560 (ttm) cc_final: 0.8303 (mtp) REVERT: E 171 MET cc_start: 0.7477 (mmm) cc_final: 0.6933 (mpt) REVERT: E 180 ARG cc_start: 0.7148 (tpt170) cc_final: 0.5283 (tmt170) REVERT: E 241 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: E 481 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: F 68 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8879 (mm) REVERT: G 68 GLU cc_start: 0.4639 (OUTLIER) cc_final: 0.3932 (mt-10) REVERT: G 173 GLU cc_start: 0.8444 (pm20) cc_final: 0.8172 (tp30) REVERT: G 261 MET cc_start: 0.8717 (mtp) cc_final: 0.8514 (mtp) REVERT: H 68 GLU cc_start: 0.5079 (OUTLIER) cc_final: 0.3256 (tp30) REVERT: H 290 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6302 (pp20) outliers start: 49 outliers final: 21 residues processed: 202 average time/residue: 1.4494 time to fit residues: 321.2859 Evaluate side-chains 203 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 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 39 SER Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 173 GLU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 329 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 121 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 182 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 167 optimal weight: 0.0370 chunk 199 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 GLN E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3635 r_free = 0.3635 target = 0.118147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096344 restraints weight = 29124.229| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.00 r_work: 0.3182 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3281 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= 0.096 Angle : 0.449 7.767 22207 Z= 0.243 Chirality : 0.041 0.187 2433 Planarity : 0.003 0.053 2930 Dihedral : 3.935 19.388 2256 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.19 % Allowed : 15.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2040 helix: 1.74 (0.20), residues: 646 sheet: -0.24 (0.22), residues: 470 loop : 0.08 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 249 HIS 0.003 0.001 HIS F 17 PHE 0.016 0.001 PHE D 510 TYR 0.008 0.001 TYR H 117 ARG 0.008 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 746) hydrogen bonds : angle 4.68041 ( 2190) covalent geometry : bond 0.00207 (16376) covalent geometry : angle 0.44917 (22207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 1.818 Fit side-chains revert: symmetry clash REVERT: B 64 SER cc_start: 0.8382 (t) cc_final: 0.7977 (p) REVERT: C 131 LYS cc_start: 0.8966 (mtpp) cc_final: 0.7827 (tmtt) REVERT: C 161 LYS cc_start: 0.9189 (tttt) cc_final: 0.8887 (ttpp) REVERT: D 44 ASN cc_start: 0.8853 (p0) cc_final: 0.8440 (p0) REVERT: D 48 MET cc_start: 0.8076 (mmt) cc_final: 0.7662 (mmp) REVERT: D 178 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7167 (mmm) REVERT: D 188 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: D 202 MET cc_start: 0.8493 (mtt) cc_final: 0.8145 (mtp) REVERT: D 216 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6872 (mtm) REVERT: D 259 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: D 347 ASP cc_start: 0.7814 (t0) cc_final: 0.7364 (p0) REVERT: D 410 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.7016 (ttp) REVERT: D 417 MET cc_start: 0.8413 (mmt) cc_final: 0.8136 (mmt) REVERT: D 500 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5960 (mt-10) REVERT: E 160 MET cc_start: 0.8498 (ttm) cc_final: 0.8250 (mtp) REVERT: E 171 MET cc_start: 0.7210 (mmm) cc_final: 0.6650 (mpt) REVERT: E 180 ARG cc_start: 0.6979 (tpt170) cc_final: 0.5062 (tmt170) REVERT: E 241 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: E 247 PHE cc_start: 0.6439 (t80) cc_final: 0.6169 (t80) REVERT: E 249 TRP cc_start: 0.5599 (t60) cc_final: 0.5359 (p-90) REVERT: E 481 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: F 31 GLN cc_start: 0.8396 (mt0) cc_final: 0.8167 (mt0) REVERT: F 68 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.8972 (mm) REVERT: G 68 GLU cc_start: 0.4377 (OUTLIER) cc_final: 0.3788 (mt-10) REVERT: G 173 GLU cc_start: 0.8424 (pm20) cc_final: 0.8062 (tp30) REVERT: G 261 MET cc_start: 0.8599 (mtp) cc_final: 0.8377 (mtp) REVERT: H 68 GLU cc_start: 0.4384 (OUTLIER) cc_final: 0.2870 (tp30) REVERT: H 112 MET cc_start: 0.8284 (ttt) cc_final: 0.7912 (ttp) REVERT: H 290 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6129 (pp20) outliers start: 37 outliers final: 16 residues processed: 221 average time/residue: 1.4987 time to fit residues: 363.9434 Evaluate side-chains 204 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 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 124 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 329 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 29 optimal weight: 0.0670 chunk 114 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN B 49 GLN D 243 GLN E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN G 125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.116285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094689 restraints weight = 29333.749| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.87 r_work: 0.3152 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16376 Z= 0.144 Angle : 0.485 7.120 22207 Z= 0.261 Chirality : 0.042 0.251 2433 Planarity : 0.003 0.051 2930 Dihedral : 4.064 22.085 2256 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.30 % Allowed : 15.96 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2040 helix: 1.68 (0.20), residues: 646 sheet: -0.26 (0.22), residues: 476 loop : 0.09 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 249 HIS 0.002 0.001 HIS F 17 PHE 0.019 0.001 PHE C 152 TYR 0.019 0.001 TYR D 458 ARG 0.010 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 746) hydrogen bonds : angle 4.77882 ( 2190) covalent geometry : bond 0.00328 (16376) covalent geometry : angle 0.48491 (22207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 3.041 Fit side-chains revert: symmetry clash REVERT: B 35 ASP cc_start: 0.7786 (t70) cc_final: 0.7525 (t70) REVERT: D 44 ASN cc_start: 0.8837 (p0) cc_final: 0.8565 (p0) REVERT: D 48 MET cc_start: 0.8046 (mmt) cc_final: 0.7629 (mmp) REVERT: D 178 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7168 (mmm) REVERT: D 202 MET cc_start: 0.8495 (mtt) cc_final: 0.8139 (mtp) REVERT: D 216 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6869 (mtm) REVERT: D 259 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: D 347 ASP cc_start: 0.7914 (t0) cc_final: 0.7449 (p0) REVERT: D 410 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6978 (ttp) REVERT: D 500 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5930 (mt-10) REVERT: E 160 MET cc_start: 0.8519 (ttm) cc_final: 0.8267 (mtp) REVERT: E 171 MET cc_start: 0.7176 (mmm) cc_final: 0.6686 (mpt) REVERT: E 178 MET cc_start: 0.0979 (OUTLIER) cc_final: -0.0755 (tpt) REVERT: E 180 ARG cc_start: 0.7069 (tpt170) cc_final: 0.5151 (tmt170) REVERT: E 241 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: E 249 TRP cc_start: 0.5633 (t60) cc_final: 0.5359 (p-90) REVERT: E 481 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: F 68 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8992 (mm) REVERT: G 68 GLU cc_start: 0.4319 (OUTLIER) cc_final: 0.3651 (mt-10) REVERT: G 261 MET cc_start: 0.8593 (mtp) cc_final: 0.8379 (mtp) REVERT: H 68 GLU cc_start: 0.4732 (OUTLIER) cc_final: 0.2894 (tp30) REVERT: H 290 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6141 (pp20) outliers start: 39 outliers final: 17 residues processed: 205 average time/residue: 1.5609 time to fit residues: 353.5001 Evaluate side-chains 200 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 481 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 329 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 15 optimal weight: 8.9990 chunk 182 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 0.3980 chunk 158 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 GLN E 174 ASN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN G 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094337 restraints weight = 29040.509| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.02 r_work: 0.3144 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16376 Z= 0.135 Angle : 0.483 7.477 22207 Z= 0.260 Chirality : 0.042 0.218 2433 Planarity : 0.003 0.050 2930 Dihedral : 4.093 22.958 2256 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.01 % Allowed : 16.08 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2040 helix: 1.73 (0.20), residues: 634 sheet: -0.27 (0.22), residues: 478 loop : 0.10 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 249 HIS 0.002 0.001 HIS F 17 PHE 0.026 0.001 PHE D 247 TYR 0.028 0.001 TYR D 458 ARG 0.010 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 746) hydrogen bonds : angle 4.77478 ( 2190) covalent geometry : bond 0.00308 (16376) covalent geometry : angle 0.48305 (22207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16106.73 seconds wall clock time: 281 minutes 0.38 seconds (16860.38 seconds total)