Starting phenix.real_space_refine on Fri Jul 3 05:53:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z2a_14459/07_2026/7z2a_14459.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2a_14459/07_2026/7z2a_14459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z2a_14459/07_2026/7z2a_14459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2a_14459/07_2026/7z2a_14459.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z2a_14459/07_2026/7z2a_14459.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z2a_14459/07_2026/7z2a_14459.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z2a_14459/07_2026/7z2a_14459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2a_14459/07_2026/7z2a_14459.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 sd= 0.012 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 65 5.16 5 C 5937 2.51 5 N 1635 2.21 5 O 1834 1.98 5 H 2765 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12244 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 5494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5494 Classifications: {'peptide': 347} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.83, per 1000 atoms: 0.15 Number of scatterers: 12244 At special positions: 0 Unit cell: (112.05, 105.3, 85.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 65 16.00 P 6 15.00 Mg 2 11.99 O 1834 8.00 N 1635 7.00 C 5937 6.00 H 2765 1.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 435.8 milliseconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 52.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.609A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.557A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.078A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.523A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.407A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.997A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.601A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.591A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.624A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.079A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 3.910A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.428A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 71 through 81 removed outlier: 4.487A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.745A pdb=" N PHE H 87 " --> pdb=" O GLY H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 108 Processing helix chain 'H' and resid 109 through 129 removed outlier: 4.294A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 Processing helix chain 'H' and resid 182 through 198 removed outlier: 3.545A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 223 through 244 removed outlier: 3.811A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 278 through 282 removed outlier: 3.604A pdb=" N GLN H 281 " --> pdb=" O ARG H 278 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN H 282 " --> pdb=" O GLY H 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 278 through 282' Processing helix chain 'H' and resid 287 through 297 removed outlier: 3.548A pdb=" N ASP H 297 " --> pdb=" O GLN H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 301 Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 384 through 401 removed outlier: 4.204A pdb=" N ARG H 401 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 411 removed outlier: 4.122A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 436 removed outlier: 4.071A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 46 through 53 Processing helix chain 'K' and resid 70 through 77 Processing helix chain 'K' and resid 79 through 88 Processing helix chain 'K' and resid 103 through 109 Processing helix chain 'K' and resid 115 through 133 removed outlier: 3.559A pdb=" N MET K 120 " --> pdb=" O GLY K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 160 Processing helix chain 'K' and resid 185 through 198 removed outlier: 3.840A pdb=" N ARG K 198 " --> pdb=" O HIS K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 287 Processing helix chain 'K' and resid 295 through 298 Processing helix chain 'K' and resid 299 through 310 removed outlier: 4.794A pdb=" N ASP K 307 " --> pdb=" O ARG K 303 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N SER K 308 " --> pdb=" O LEU K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 326 No H-bonds generated for 'chain 'K' and resid 324 through 326' Processing helix chain 'K' and resid 327 through 343 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.018A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.815A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.910A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU H 3 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY H 134 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER H 140 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.171A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER H 374 " --> pdb=" O PHE H 319 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE H 319 " --> pdb=" O SER H 374 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR H 376 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA H 317 " --> pdb=" O THR H 376 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE H 378 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL H 315 " --> pdb=" O ILE H 378 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN H 380 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU H 248 " --> pdb=" O VAL H 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.891A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 63 through 65 removed outlier: 9.069A pdb=" N TYR K 63 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL K 8 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE K 65 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE K 10 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR K 93 " --> pdb=" O LEU K 316 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE K 318 " --> pdb=" O THR K 93 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE K 95 " --> pdb=" O ILE K 318 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASN K 320 " --> pdb=" O PHE K 95 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR K 97 " --> pdb=" O ASN K 320 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER K 92 " --> pdb=" O CYS K 241 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE K 243 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL K 94 " --> pdb=" O ILE K 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 63 through 65 removed outlier: 9.069A pdb=" N TYR K 63 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL K 8 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE K 65 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE K 10 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR K 93 " --> pdb=" O LEU K 316 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE K 318 " --> pdb=" O THR K 93 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE K 95 " --> pdb=" O ILE K 318 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASN K 320 " --> pdb=" O PHE K 95 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR K 97 " --> pdb=" O ASN K 320 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER K 92 " --> pdb=" O CYS K 241 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE K 243 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL K 94 " --> pdb=" O ILE K 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.536A pdb=" N MET K 35 " --> pdb=" O MET K 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 165 through 167 Processing sheet with id=AB1, first strand: chain 'K' and resid 202 through 205 removed outlier: 4.981A pdb=" N GLU K 203 " --> pdb=" O THR K 210 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR K 210 " --> pdb=" O GLU K 203 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1461 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: 2.04 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 2758 1.13 - 1.31: 1625 1.31 - 1.48: 3888 1.48 - 1.66: 4056 1.66 - 1.83: 105 Bond restraints: 12432 Sorted by residual: bond pdb=" NE ARG K 297 " pdb=" HE ARG K 297 " ideal model delta sigma weight residual 0.860 1.050 -0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" NH1 ARG K 58 " pdb="HH11 ARG K 58 " ideal model delta sigma weight residual 0.860 1.045 -0.185 2.00e-02 2.50e+03 8.54e+01 bond pdb=" NH1 ARG K 213 " pdb="HH11 ARG K 213 " ideal model delta sigma weight residual 0.860 1.044 -0.184 2.00e-02 2.50e+03 8.44e+01 bond pdb=" NH2 ARG K 58 " pdb="HH21 ARG K 58 " ideal model delta sigma weight residual 0.860 1.039 -0.179 2.00e-02 2.50e+03 7.97e+01 bond pdb=" NE ARG K 53 " pdb=" HE ARG K 53 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.83e+01 ... (remaining 12427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 17867 3.07 - 6.14: 1276 6.14 - 9.21: 218 9.21 - 12.28: 15 12.28 - 15.35: 8 Bond angle restraints: 19384 Sorted by residual: angle pdb=" C LYS K 139 " pdb=" N ILE K 140 " pdb=" CA ILE K 140 " ideal model delta sigma weight residual 122.48 113.87 8.61 1.25e+00 6.40e-01 4.75e+01 angle pdb=" C SER K 322 " pdb=" N PRO K 323 " pdb=" CA PRO K 323 " ideal model delta sigma weight residual 119.87 126.71 -6.84 1.04e+00 9.25e-01 4.33e+01 angle pdb=" N PRO K 169 " pdb=" CA PRO K 169 " pdb=" C PRO K 169 " ideal model delta sigma weight residual 111.03 100.91 10.12 1.54e+00 4.22e-01 4.32e+01 angle pdb=" C ASN K 157 " pdb=" N PRO K 158 " pdb=" CA PRO K 158 " ideal model delta sigma weight residual 119.82 126.20 -6.38 9.80e-01 1.04e+00 4.23e+01 angle pdb=" N ILE K 152 " pdb=" CA ILE K 152 " pdb=" C ILE K 152 " ideal model delta sigma weight residual 107.80 117.01 -9.21 1.45e+00 4.76e-01 4.03e+01 ... (remaining 19379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.62: 6505 33.62 - 67.24: 148 67.24 - 100.86: 15 100.86 - 134.48: 0 134.48 - 168.09: 3 Dihedral angle restraints: 6671 sinusoidal: 3084 harmonic: 3587 Sorted by residual: dihedral pdb=" CD2 HIS K 332 " pdb=" CG HIS K 332 " pdb=" ND1 HIS K 332 " pdb=" HD1 HIS K 332 " ideal model delta harmonic sigma weight residual -180.00 -136.41 -43.59 0 5.00e+00 4.00e-02 7.60e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.64 -168.09 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -51.70 156.29 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 6668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 989 0.079 - 0.159: 343 0.159 - 0.238: 97 0.238 - 0.317: 22 0.317 - 0.396: 3 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CA HIS A 197 " pdb=" N HIS A 197 " pdb=" C HIS A 197 " pdb=" CB HIS A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C3' G2P H 501 " pdb=" C2' G2P H 501 " pdb=" C4' G2P H 501 " pdb=" O3' G2P H 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.38 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA THR H 109 " pdb=" N THR H 109 " pdb=" C THR H 109 " pdb=" CB THR H 109 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1451 not shown) Planarity restraints: 2040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 332 " 0.153 2.00e-02 2.50e+03 1.62e-01 5.90e+02 pdb=" CG HIS K 332 " 0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS K 332 " 0.148 2.00e-02 2.50e+03 pdb=" CD2 HIS K 332 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 HIS K 332 " 0.082 2.00e-02 2.50e+03 pdb=" NE2 HIS K 332 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 HIS K 332 " -0.381 2.00e-02 2.50e+03 pdb=" HD2 HIS K 332 " -0.123 2.00e-02 2.50e+03 pdb=" HE1 HIS K 332 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 4 " -0.072 2.00e-02 2.50e+03 2.85e-02 2.44e+01 pdb=" CG TYR K 4 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR K 4 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR K 4 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR K 4 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR K 4 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR K 4 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR K 4 " -0.048 2.00e-02 2.50e+03 pdb=" HD1 TYR K 4 " 0.016 2.00e-02 2.50e+03 pdb=" HD2 TYR K 4 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR K 4 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR K 4 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 75 " 0.070 2.00e-02 2.50e+03 2.79e-02 2.34e+01 pdb=" CG TYR K 75 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR K 75 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR K 75 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR K 75 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR K 75 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR K 75 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR K 75 " 0.038 2.00e-02 2.50e+03 pdb=" HD1 TYR K 75 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 TYR K 75 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TYR K 75 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR K 75 " -0.011 2.00e-02 2.50e+03 ... (remaining 2037 not shown) Histogram of nonbonded interaction distances: 0.27 - 1.13: 8 1.13 - 2.00: 263 2.00 - 2.87: 15664 2.87 - 3.73: 39212 3.73 - 4.60: 69387 Warning: very small nonbonded interaction distances. Nonbonded interactions: 124534 Sorted by model distance: nonbonded pdb=" OD1 ASP A 431 " pdb="HG11 VAL K 48 " model vdw 0.268 2.620 nonbonded pdb=" CG GLU A 415 " pdb="HH12 ARG K 340 " model vdw 0.813 2.200 nonbonded pdb=" OD1 ASP A 431 " pdb=" CG1 VAL K 48 " model vdw 0.925 3.100 nonbonded pdb=" OE1 GLU A 434 " pdb=" OE1 GLN K 51 " model vdw 0.946 2.800 nonbonded pdb=" OE2 GLU H 431 " pdb=" HD2 PHE K 293 " model vdw 1.011 2.450 ... (remaining 124529 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.040 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: 0.100 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 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 0.313 9671 Z= 0.860 Angle : 1.594 14.069 13103 Z= 1.079 Chirality : 0.089 0.396 1454 Planarity : 0.008 0.074 1703 Dihedral : 14.601 168.095 3578 Min Nonbonded Distance : 0.925 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.85 % Favored : 96.98 % Rotamer: Outliers : 0.48 % Allowed : 5.03 % Favored : 94.49 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.23), residues: 1193 helix: 0.65 (0.20), residues: 518 sheet: -0.23 (0.36), residues: 209 loop : -0.49 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 260 TYR 0.064 0.006 TYR K 4 PHE 0.033 0.004 PHE K 179 TRP 0.017 0.003 TRP A 21 HIS 0.014 0.002 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.01205 / 0.72 ( 9667) covalent geometry : angle 1.59422 / 1.08 (13103) hydrogen bonds : bond 0.18695 / 12.25 ( 481) hydrogen bonds : angle 7.60444 / 5.73 ( 1461) Misc. bond : bond 0.23315 / 11.73 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 254 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.5696 (t0) cc_final: 0.5141 (t0) REVERT: A 210 TYR cc_start: 0.8635 (m-80) cc_final: 0.8201 (m-10) REVERT: A 295 CYS cc_start: 0.7822 (m) cc_final: 0.7316 (m) REVERT: A 380 ASN cc_start: 0.6409 (t0) cc_final: 0.5941 (t0) REVERT: H 20 PHE cc_start: 0.7661 (t80) cc_final: 0.7378 (t80) REVERT: H 75 MET cc_start: 0.7827 (mmp) cc_final: 0.7606 (mmp) REVERT: H 156 LYS cc_start: 0.9195 (mmtm) cc_final: 0.8673 (mtmt) REVERT: K 190 MET cc_start: 0.7063 (ttp) cc_final: 0.6426 (tmm) outliers start: 5 outliers final: 1 residues processed: 258 average time/residue: 0.1196 time to fit residues: 42.6914 Evaluate side-chains 130 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 101 ASN A 226 ASN A 300 ASN A 406 HIS H 11 GLN H 15 GLN H 28 HIS H 37 HIS ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 197 ASN H 247 GLN ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 HIS ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.073786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.052876 restraints weight = 70460.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.055355 restraints weight = 37148.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.056979 restraints weight = 24046.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.058087 restraints weight = 17835.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.058734 restraints weight = 14524.681| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9671 Z= 0.232 Angle : 0.708 8.022 13103 Z= 0.381 Chirality : 0.044 0.173 1454 Planarity : 0.006 0.084 1703 Dihedral : 9.823 175.428 1322 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 31.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 0.10 % Allowed : 1.84 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1193 helix: 1.21 (0.21), residues: 532 sheet: 0.13 (0.36), residues: 213 loop : -0.51 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 340 TYR 0.020 0.002 TYR K 75 PHE 0.025 0.002 PHE K 144 TRP 0.010 0.001 TRP H 407 HIS 0.008 0.002 HIS H 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.23 ( 9667) covalent geometry : angle 0.70844 / 0.38 (13103) hydrogen bonds : bond 0.05254 / 3.76 ( 481) hydrogen bonds : angle 5.63201 / 4.07 ( 1461) Misc. bond : bond 0.00221 / 0.12 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.7351 (t0) cc_final: 0.6962 (t0) REVERT: A 245 ASP cc_start: 0.7947 (t70) cc_final: 0.7377 (t0) REVERT: A 302 MET cc_start: 0.9371 (mmp) cc_final: 0.9078 (mpp) REVERT: A 317 LEU cc_start: 0.8867 (mm) cc_final: 0.8549 (mp) REVERT: A 351 PHE cc_start: 0.7656 (m-80) cc_final: 0.7046 (m-80) REVERT: H 37 HIS cc_start: 0.8537 (m-70) cc_final: 0.8323 (m-70) REVERT: H 160 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8261 (mt-10) REVERT: H 194 LEU cc_start: 0.9490 (mt) cc_final: 0.9278 (mt) REVERT: H 267 PHE cc_start: 0.8945 (m-80) cc_final: 0.8712 (m-80) REVERT: H 295 MET cc_start: 0.8902 (ptp) cc_final: 0.8503 (ttm) REVERT: H 302 MET cc_start: 0.7761 (mtm) cc_final: 0.6952 (mtt) REVERT: H 325 MET cc_start: 0.8265 (mmt) cc_final: 0.7844 (mmm) REVERT: H 342 TYR cc_start: 0.8160 (m-10) cc_final: 0.7893 (m-10) REVERT: H 425 MET cc_start: 0.9052 (tpp) cc_final: 0.8840 (tpp) REVERT: K 95 PHE cc_start: 0.9532 (m-10) cc_final: 0.9306 (m-80) REVERT: K 144 PHE cc_start: 0.8988 (t80) cc_final: 0.8261 (t80) REVERT: K 215 HIS cc_start: 0.8893 (m-70) cc_final: 0.8151 (m-70) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1152 time to fit residues: 25.2179 Evaluate side-chains 107 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 51 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 30.0000 chunk 29 optimal weight: 0.3980 chunk 90 optimal weight: 40.0000 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 HIS A 228 ASN H 14 ASN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 ASN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.073292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.052602 restraints weight = 70368.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.055033 restraints weight = 37084.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.056623 restraints weight = 23965.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.057691 restraints weight = 17723.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.058310 restraints weight = 14435.263| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 9671 Z= 0.145 Angle : 0.577 14.386 13103 Z= 0.313 Chirality : 0.041 0.152 1454 Planarity : 0.007 0.256 1703 Dihedral : 10.393 179.463 1322 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 33.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.25), residues: 1193 helix: 1.64 (0.23), residues: 527 sheet: -0.07 (0.36), residues: 209 loop : -0.36 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG K 297 TYR 0.018 0.001 TYR A 357 PHE 0.012 0.001 PHE K 144 TRP 0.012 0.001 TRP H 21 HIS 0.007 0.001 HIS H 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 ( 9667) covalent geometry : angle 0.57650 / 0.31 (13103) hydrogen bonds : bond 0.04830 / 3.35 ( 481) hydrogen bonds : angle 5.24309 / 3.77 ( 1461) Misc. bond : bond 0.00260 / 0.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8596 (t0) cc_final: 0.8378 (t0) REVERT: A 136 LEU cc_start: 0.9154 (mp) cc_final: 0.8748 (mp) REVERT: A 205 ASP cc_start: 0.7396 (t0) cc_final: 0.6975 (t0) REVERT: A 210 TYR cc_start: 0.8831 (m-80) cc_final: 0.8589 (m-80) REVERT: A 302 MET cc_start: 0.9314 (mmp) cc_final: 0.9043 (mmt) REVERT: A 317 LEU cc_start: 0.8896 (mm) cc_final: 0.8612 (mp) REVERT: A 351 PHE cc_start: 0.7710 (m-80) cc_final: 0.7004 (m-80) REVERT: H 37 HIS cc_start: 0.8520 (m-70) cc_final: 0.8299 (m-70) REVERT: H 230 LEU cc_start: 0.9494 (tp) cc_final: 0.9257 (tp) REVERT: H 325 MET cc_start: 0.8052 (mmt) cc_final: 0.7503 (mmm) REVERT: H 372 LYS cc_start: 0.8803 (mptt) cc_final: 0.8499 (mmtm) REVERT: K 6 MET cc_start: 0.5818 (tpp) cc_final: 0.5094 (tpp) REVERT: K 144 PHE cc_start: 0.8945 (t80) cc_final: 0.8153 (t80) REVERT: K 190 MET cc_start: 0.9261 (tmm) cc_final: 0.8787 (tmm) REVERT: K 215 HIS cc_start: 0.8887 (m-70) cc_final: 0.8167 (m-70) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1037 time to fit residues: 20.9736 Evaluate side-chains 105 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 81 optimal weight: 40.0000 chunk 67 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN ** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.071883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.051208 restraints weight = 69929.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.053551 restraints weight = 36594.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.055065 restraints weight = 23637.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056059 restraints weight = 17585.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.056646 restraints weight = 14408.411| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9671 Z= 0.149 Angle : 0.532 7.249 13103 Z= 0.288 Chirality : 0.041 0.284 1454 Planarity : 0.010 0.385 1703 Dihedral : 10.024 178.424 1322 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 36.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.25), residues: 1193 helix: 1.68 (0.23), residues: 530 sheet: -0.12 (0.36), residues: 211 loop : -0.31 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG K 297 TYR 0.017 0.001 TYR K 75 PHE 0.014 0.001 PHE H 262 TRP 0.010 0.001 TRP H 21 HIS 0.008 0.001 HIS H 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 ( 9667) covalent geometry : angle 0.53170 / 0.29 (13103) hydrogen bonds : bond 0.04181 / 2.90 ( 481) hydrogen bonds : angle 5.08819 / 3.64 ( 1461) Misc. bond : bond 0.00661 / 0.33 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8611 (t0) cc_final: 0.8402 (t0) REVERT: A 205 ASP cc_start: 0.7632 (t0) cc_final: 0.7258 (t0) REVERT: A 317 LEU cc_start: 0.8973 (mm) cc_final: 0.8773 (mp) REVERT: A 351 PHE cc_start: 0.7824 (m-80) cc_final: 0.7158 (m-80) REVERT: H 37 HIS cc_start: 0.8517 (m-70) cc_final: 0.8294 (m-70) REVERT: H 181 VAL cc_start: 0.8956 (t) cc_final: 0.8734 (p) REVERT: H 230 LEU cc_start: 0.9447 (tp) cc_final: 0.9217 (tt) REVERT: H 372 LYS cc_start: 0.8803 (mptt) cc_final: 0.8530 (mmtm) REVERT: K 6 MET cc_start: 0.5986 (tpp) cc_final: 0.5364 (tpp) REVERT: K 95 PHE cc_start: 0.9458 (m-10) cc_final: 0.9250 (m-80) REVERT: K 144 PHE cc_start: 0.8970 (t80) cc_final: 0.8220 (t80) REVERT: K 215 HIS cc_start: 0.8936 (m-70) cc_final: 0.8268 (m-70) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1028 time to fit residues: 20.9393 Evaluate side-chains 94 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 40.0000 chunk 104 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 55 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.068295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.047777 restraints weight = 73565.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049907 restraints weight = 39210.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051315 restraints weight = 25628.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.052255 restraints weight = 19210.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.052864 restraints weight = 15819.458| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9671 Z= 0.214 Angle : 0.596 7.370 13103 Z= 0.318 Chirality : 0.041 0.209 1454 Planarity : 0.010 0.362 1703 Dihedral : 10.186 179.014 1322 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 42.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1193 helix: 1.47 (0.23), residues: 538 sheet: -0.12 (0.37), residues: 195 loop : -0.36 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 297 TYR 0.016 0.002 TYR A 319 PHE 0.013 0.002 PHE K 144 TRP 0.007 0.001 TRP H 21 HIS 0.006 0.002 HIS H 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 ( 9667) covalent geometry : angle 0.59554 / 0.32 (13103) hydrogen bonds : bond 0.04190 / 2.88 ( 481) hydrogen bonds : angle 5.18374 / 3.72 ( 1461) Misc. bond : bond 0.00346 / 0.18 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 VAL cc_start: 0.9609 (m) cc_final: 0.9315 (p) REVERT: H 37 HIS cc_start: 0.8722 (m-70) cc_final: 0.8426 (m-70) REVERT: H 50 ASN cc_start: 0.8664 (p0) cc_final: 0.8369 (p0) REVERT: H 230 LEU cc_start: 0.9430 (tp) cc_final: 0.9228 (tp) REVERT: H 290 GLU cc_start: 0.7833 (tp30) cc_final: 0.7491 (tp30) REVERT: H 323 MET cc_start: 0.6861 (mtm) cc_final: 0.6121 (mtm) REVERT: H 372 LYS cc_start: 0.8899 (mptt) cc_final: 0.8692 (mmtm) REVERT: K 144 PHE cc_start: 0.9051 (t80) cc_final: 0.8267 (t80) REVERT: K 215 HIS cc_start: 0.9094 (m-70) cc_final: 0.8787 (m-70) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1263 time to fit residues: 22.5326 Evaluate side-chains 93 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 77 optimal weight: 0.4980 chunk 99 optimal weight: 30.0000 chunk 109 optimal weight: 40.0000 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 chunk 75 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 95 optimal weight: 50.0000 chunk 53 optimal weight: 0.9980 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.068707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.048335 restraints weight = 71508.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.050593 restraints weight = 36280.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.052073 restraints weight = 23067.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.053034 restraints weight = 16978.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053583 restraints weight = 13879.867| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9671 Z= 0.134 Angle : 0.497 6.915 13103 Z= 0.267 Chirality : 0.039 0.138 1454 Planarity : 0.009 0.364 1703 Dihedral : 10.155 179.834 1322 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 42.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1193 helix: 1.77 (0.23), residues: 530 sheet: -0.22 (0.37), residues: 201 loop : -0.22 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 297 TYR 0.014 0.001 TYR K 75 PHE 0.013 0.001 PHE K 144 TRP 0.012 0.002 TRP H 21 HIS 0.005 0.001 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 9667) covalent geometry : angle 0.49687 / 0.27 (13103) hydrogen bonds : bond 0.03729 / 2.60 ( 481) hydrogen bonds : angle 4.91765 / 3.52 ( 1461) Misc. bond : bond 0.00277 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 VAL cc_start: 0.9583 (m) cc_final: 0.9284 (p) REVERT: A 351 PHE cc_start: 0.7432 (m-80) cc_final: 0.7035 (m-80) REVERT: H 37 HIS cc_start: 0.8687 (m-70) cc_final: 0.8468 (m-70) REVERT: H 50 ASN cc_start: 0.8689 (p0) cc_final: 0.8374 (p0) REVERT: H 275 LEU cc_start: 0.9292 (mt) cc_final: 0.9045 (mp) REVERT: H 290 GLU cc_start: 0.7694 (tp30) cc_final: 0.7409 (tp30) REVERT: H 295 MET cc_start: 0.8427 (ttm) cc_final: 0.8117 (ttm) REVERT: H 323 MET cc_start: 0.6482 (mtm) cc_final: 0.6157 (mtt) REVERT: H 413 MET cc_start: 0.7923 (mmt) cc_final: 0.6683 (mmt) REVERT: K 144 PHE cc_start: 0.8974 (t80) cc_final: 0.8228 (t80) REVERT: K 215 HIS cc_start: 0.9103 (m-70) cc_final: 0.8784 (m-70) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1084 time to fit residues: 19.3550 Evaluate side-chains 94 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 40.0000 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 108 optimal weight: 50.0000 chunk 40 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 overall best weight: 3.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.068551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.048330 restraints weight = 71740.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.050503 restraints weight = 37390.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.051933 restraints weight = 24059.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.052882 restraints weight = 17847.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.053408 restraints weight = 14658.659| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9671 Z= 0.127 Angle : 0.476 6.463 13103 Z= 0.254 Chirality : 0.039 0.202 1454 Planarity : 0.009 0.343 1703 Dihedral : 10.132 178.684 1322 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 42.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.25), residues: 1193 helix: 1.93 (0.23), residues: 530 sheet: -0.24 (0.37), residues: 203 loop : -0.13 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 297 TYR 0.015 0.001 TYR A 224 PHE 0.013 0.001 PHE K 144 TRP 0.007 0.001 TRP H 21 HIS 0.003 0.001 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 9667) covalent geometry : angle 0.47554 / 0.25 (13103) hydrogen bonds : bond 0.03538 / 2.45 ( 481) hydrogen bonds : angle 4.76558 / 3.43 ( 1461) Misc. bond : bond 0.00275 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8730 (t0) cc_final: 0.8493 (t0) REVERT: A 118 VAL cc_start: 0.9581 (m) cc_final: 0.9280 (p) REVERT: H 37 HIS cc_start: 0.8705 (m-70) cc_final: 0.8498 (m-70) REVERT: H 50 ASN cc_start: 0.8607 (p0) cc_final: 0.8371 (p0) REVERT: H 235 MET cc_start: 0.9164 (mtp) cc_final: 0.8931 (mtt) REVERT: H 275 LEU cc_start: 0.9311 (mt) cc_final: 0.9045 (mp) REVERT: H 290 GLU cc_start: 0.7882 (tp30) cc_final: 0.7571 (tp30) REVERT: H 295 MET cc_start: 0.8543 (ttm) cc_final: 0.8166 (ttm) REVERT: H 309 HIS cc_start: 0.9230 (m-70) cc_final: 0.9023 (m-70) REVERT: H 413 MET cc_start: 0.7910 (mmt) cc_final: 0.6839 (mmt) REVERT: K 95 PHE cc_start: 0.9517 (m-80) cc_final: 0.9167 (m-80) REVERT: K 144 PHE cc_start: 0.9014 (t80) cc_final: 0.8325 (t80) REVERT: K 215 HIS cc_start: 0.9186 (m-70) cc_final: 0.8335 (m-70) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1107 time to fit residues: 19.1286 Evaluate side-chains 95 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 14 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 94 optimal weight: 40.0000 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.066910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.046973 restraints weight = 71981.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.049156 restraints weight = 36507.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.050582 restraints weight = 23118.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.051516 restraints weight = 17001.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.052039 restraints weight = 13880.393| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9671 Z= 0.171 Angle : 0.523 8.534 13103 Z= 0.279 Chirality : 0.039 0.153 1454 Planarity : 0.009 0.335 1703 Dihedral : 10.339 179.854 1322 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 46.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.94 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.25), residues: 1193 helix: 1.83 (0.23), residues: 531 sheet: -0.33 (0.37), residues: 207 loop : -0.20 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 297 TYR 0.014 0.001 TYR K 75 PHE 0.012 0.001 PHE K 144 TRP 0.010 0.001 TRP H 407 HIS 0.004 0.001 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 ( 9667) covalent geometry : angle 0.52259 / 0.28 (13103) hydrogen bonds : bond 0.03578 / 2.49 ( 481) hydrogen bonds : angle 4.80300 / 3.43 ( 1461) Misc. bond : bond 0.00269 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 VAL cc_start: 0.9476 (t) cc_final: 0.9222 (p) REVERT: A 76 ASP cc_start: 0.8646 (t0) cc_final: 0.8438 (t0) REVERT: A 118 VAL cc_start: 0.9577 (m) cc_final: 0.9251 (p) REVERT: A 245 ASP cc_start: 0.7954 (p0) cc_final: 0.7492 (p0) REVERT: H 50 ASN cc_start: 0.8696 (p0) cc_final: 0.8479 (p0) REVERT: H 235 MET cc_start: 0.9249 (mtp) cc_final: 0.9037 (mtm) REVERT: H 269 MET cc_start: 0.8319 (ttt) cc_final: 0.7984 (tmm) REVERT: H 290 GLU cc_start: 0.7853 (tp30) cc_final: 0.7593 (tp30) REVERT: H 295 MET cc_start: 0.8462 (ttm) cc_final: 0.8233 (ttm) REVERT: H 301 MET cc_start: 0.8596 (mmp) cc_final: 0.8231 (mmp) REVERT: H 372 LYS cc_start: 0.8942 (mptt) cc_final: 0.8699 (mmtm) REVERT: H 413 MET cc_start: 0.7775 (mmt) cc_final: 0.7178 (mmp) REVERT: K 144 PHE cc_start: 0.8998 (t80) cc_final: 0.8332 (t80) REVERT: K 153 CYS cc_start: 0.8957 (t) cc_final: 0.8596 (m) REVERT: K 215 HIS cc_start: 0.9177 (m-70) cc_final: 0.8236 (m-70) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0960 time to fit residues: 17.4707 Evaluate side-chains 93 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 9 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 117 optimal weight: 30.0000 chunk 61 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 5 optimal weight: 0.0870 chunk 103 optimal weight: 30.0000 chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.066927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.046844 restraints weight = 72559.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.048954 restraints weight = 37799.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.050341 restraints weight = 24340.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051249 restraints weight = 18083.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.051758 restraints weight = 14902.695| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.6778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9671 Z= 0.145 Angle : 0.492 7.398 13103 Z= 0.266 Chirality : 0.039 0.139 1454 Planarity : 0.008 0.313 1703 Dihedral : 10.336 178.889 1322 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 45.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.26), residues: 1193 helix: 1.97 (0.23), residues: 523 sheet: -0.37 (0.37), residues: 207 loop : -0.28 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 297 TYR 0.012 0.001 TYR K 75 PHE 0.012 0.001 PHE K 144 TRP 0.014 0.001 TRP H 21 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 9667) covalent geometry : angle 0.49247 / 0.27 (13103) hydrogen bonds : bond 0.03470 / 2.41 ( 481) hydrogen bonds : angle 4.77985 / 3.44 ( 1461) Misc. bond : bond 0.00274 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 VAL cc_start: 0.9467 (t) cc_final: 0.9168 (p) REVERT: A 118 VAL cc_start: 0.9573 (m) cc_final: 0.9278 (p) REVERT: A 245 ASP cc_start: 0.8077 (p0) cc_final: 0.7617 (p0) REVERT: H 50 ASN cc_start: 0.8739 (p0) cc_final: 0.8511 (p0) REVERT: H 235 MET cc_start: 0.9261 (mtp) cc_final: 0.9041 (mtt) REVERT: H 290 GLU cc_start: 0.7939 (tp30) cc_final: 0.7571 (tp30) REVERT: H 295 MET cc_start: 0.8529 (ttm) cc_final: 0.8275 (ttm) REVERT: H 309 HIS cc_start: 0.9240 (m-70) cc_final: 0.9020 (m-70) REVERT: H 372 LYS cc_start: 0.9024 (mptt) cc_final: 0.8779 (mmtm) REVERT: H 413 MET cc_start: 0.7881 (mmt) cc_final: 0.6840 (mmt) REVERT: K 144 PHE cc_start: 0.9074 (t80) cc_final: 0.8390 (t80) REVERT: K 153 CYS cc_start: 0.8998 (t) cc_final: 0.8630 (m) REVERT: K 215 HIS cc_start: 0.9221 (m-70) cc_final: 0.8255 (m-70) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0984 time to fit residues: 16.8907 Evaluate side-chains 98 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 40.0000 chunk 86 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 35 optimal weight: 0.0470 chunk 83 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 overall best weight: 8.8088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.065561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045734 restraints weight = 74177.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.047757 restraints weight = 38557.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049068 restraints weight = 24956.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.049932 restraints weight = 18722.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.050494 restraints weight = 15498.473| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9671 Z= 0.232 Angle : 0.598 8.469 13103 Z= 0.319 Chirality : 0.040 0.145 1454 Planarity : 0.008 0.306 1703 Dihedral : 10.394 175.498 1322 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 53.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1193 helix: 1.58 (0.23), residues: 525 sheet: -0.69 (0.37), residues: 194 loop : -0.52 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 308 TYR 0.019 0.002 TYR A 319 PHE 0.014 0.002 PHE A 255 TRP 0.013 0.002 TRP A 388 HIS 0.005 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.23 ( 9667) covalent geometry : angle 0.59800 / 0.32 (13103) hydrogen bonds : bond 0.03708 / 2.56 ( 481) hydrogen bonds : angle 5.01756 / 3.60 ( 1461) Misc. bond : bond 0.00276 / 0.14 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 VAL cc_start: 0.9519 (t) cc_final: 0.9204 (p) REVERT: A 118 VAL cc_start: 0.9563 (m) cc_final: 0.9235 (p) REVERT: A 267 PHE cc_start: 0.8931 (m-80) cc_final: 0.8547 (m-10) REVERT: A 339 ARG cc_start: 0.8820 (mmm160) cc_final: 0.8555 (mmp80) REVERT: H 116 ASP cc_start: 0.8770 (t0) cc_final: 0.8443 (t0) REVERT: H 269 MET cc_start: 0.8296 (ttt) cc_final: 0.7975 (tmm) REVERT: H 290 GLU cc_start: 0.7776 (tp30) cc_final: 0.7509 (tp30) REVERT: H 309 HIS cc_start: 0.9141 (m-70) cc_final: 0.8876 (m-70) REVERT: H 413 MET cc_start: 0.7642 (mmt) cc_final: 0.6664 (mmt) REVERT: K 144 PHE cc_start: 0.9047 (t80) cc_final: 0.8362 (t80) REVERT: K 153 CYS cc_start: 0.8931 (t) cc_final: 0.8617 (m) REVERT: K 215 HIS cc_start: 0.9235 (m-70) cc_final: 0.8211 (m-70) REVERT: K 241 CYS cc_start: 0.8027 (t) cc_final: 0.7648 (t) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1331 time to fit residues: 21.5205 Evaluate side-chains 90 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 12 optimal weight: 0.6980 chunk 84 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.066458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.046385 restraints weight = 72408.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048422 restraints weight = 37591.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.049757 restraints weight = 24402.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.050595 restraints weight = 18299.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051165 restraints weight = 15257.101| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.7170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9671 Z= 0.143 Angle : 0.504 8.236 13103 Z= 0.270 Chirality : 0.039 0.142 1454 Planarity : 0.008 0.285 1703 Dihedral : 10.216 172.116 1322 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 48.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.25), residues: 1193 helix: 1.76 (0.23), residues: 525 sheet: -0.71 (0.37), residues: 195 loop : -0.46 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 123 TYR 0.011 0.001 TYR K 75 PHE 0.012 0.001 PHE K 144 TRP 0.013 0.001 TRP H 21 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 9667) covalent geometry : angle 0.50376 / 0.27 (13103) hydrogen bonds : bond 0.03484 / 2.42 ( 481) hydrogen bonds : angle 4.87715 / 3.49 ( 1461) Misc. bond : bond 0.00274 / 0.14 ( 4) =============================================================================== Job complete usr+sys time: 1707.85 seconds wall clock time: 30 minutes 29.72 seconds (1829.72 seconds total)