Starting phenix.real_space_refine on Wed Jul 30 14:15:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2a_14459/07_2025/7z2a_14459.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2a_14459/07_2025/7z2a_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_2025/7z2a_14459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2a_14459/07_2025/7z2a_14459.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2a_14459/07_2025/7z2a_14459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2a_14459/07_2025/7z2a_14459.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.75, per 1000 atoms: 0.55 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: 3.44 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.39 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: 4.62 Time building geometry restraints manager: 3.94 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: 6526 33.62 - 67.24: 153 67.24 - 100.86: 17 100.86 - 134.48: 0 134.48 - 168.09: 3 Dihedral angle restraints: 6699 sinusoidal: 3112 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 6696 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: 0.030 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: 0.270 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.130 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 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 : 14.753 168.095 3606 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (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 TRP 0.017 0.003 TRP A 21 HIS 0.014 0.002 HIS A 88 PHE 0.033 0.004 PHE K 179 TYR 0.064 0.006 TYR K 4 ARG 0.006 0.001 ARG K 260 Details of bonding type rmsd hydrogen bonds : bond 0.18695 ( 481) hydrogen bonds : angle 7.60444 ( 1461) covalent geometry : bond 0.01205 ( 9667) covalent geometry : angle 1.59422 (13103) Misc. bond : bond 0.23315 ( 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 : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.5696 (t0) cc_final: 0.5146 (t0) REVERT: A 210 TYR cc_start: 0.8635 (m-80) cc_final: 0.8204 (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: 0.5944 (t0) REVERT: H 20 PHE cc_start: 0.7661 (t80) cc_final: 0.7374 (t80) REVERT: H 75 MET cc_start: 0.7827 (mmp) cc_final: 0.7618 (mmp) REVERT: H 156 LYS cc_start: 0.9195 (mmtm) cc_final: 0.8705 (mtmt) REVERT: K 190 MET cc_start: 0.7063 (ttp) cc_final: 0.6440 (tmm) REVERT: K 215 HIS cc_start: 0.5900 (m-70) cc_final: 0.5255 (m-70) outliers start: 5 outliers final: 0 residues processed: 258 average time/residue: 0.3238 time to fit residues: 113.5837 Evaluate side-chains 131 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN A 300 ASN A 406 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 385 GLN H 406 HIS H 433 GLN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.074672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.053855 restraints weight = 69907.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056361 restraints weight = 36880.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.058044 restraints weight = 23902.473| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9671 Z= 0.207 Angle : 0.670 6.734 13103 Z= 0.364 Chirality : 0.043 0.172 1454 Planarity : 0.005 0.076 1703 Dihedral : 10.565 175.402 1350 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 29.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.15 % Rotamer: Outliers : 0.10 % Allowed : 1.35 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1193 helix: 1.34 (0.22), residues: 532 sheet: 0.15 (0.36), residues: 211 loop : -0.43 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 407 HIS 0.007 0.001 HIS H 139 PHE 0.025 0.002 PHE K 144 TYR 0.021 0.002 TYR K 75 ARG 0.006 0.001 ARG K 340 Details of bonding type rmsd hydrogen bonds : bond 0.05275 ( 481) hydrogen bonds : angle 5.59860 ( 1461) covalent geometry : bond 0.00418 ( 9667) covalent geometry : angle 0.66988 (13103) Misc. bond : bond 0.00233 ( 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 158 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.189 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 136 LEU cc_start: 0.9193 (mp) cc_final: 0.8840 (mp) REVERT: A 205 ASP cc_start: 0.7265 (t0) cc_final: 0.6765 (t0) REVERT: A 245 ASP cc_start: 0.8066 (t70) cc_final: 0.7448 (t0) REVERT: A 302 MET cc_start: 0.9365 (mmp) cc_final: 0.9129 (mmm) REVERT: A 351 PHE cc_start: 0.7647 (m-80) cc_final: 0.7284 (m-80) REVERT: H 37 HIS cc_start: 0.8609 (m-70) cc_final: 0.8356 (m-70) REVERT: H 160 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8247 (mt-10) REVERT: H 295 MET cc_start: 0.8916 (ptp) cc_final: 0.8567 (ttm) REVERT: H 302 MET cc_start: 0.7719 (mtm) cc_final: 0.6956 (mtt) REVERT: H 325 MET cc_start: 0.8206 (mmt) cc_final: 0.7813 (mmm) REVERT: H 342 TYR cc_start: 0.8099 (m-10) cc_final: 0.7819 (m-10) REVERT: H 373 MET cc_start: 0.7460 (ttm) cc_final: 0.7162 (ttp) REVERT: K 144 PHE cc_start: 0.9005 (t80) cc_final: 0.8236 (t80) REVERT: K 215 HIS cc_start: 0.9073 (m-70) cc_final: 0.8428 (m-70) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.3203 time to fit residues: 69.5911 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 : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 9 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 61 HIS H 11 GLN H 15 GLN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 GLN ** H 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.071178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050628 restraints weight = 71421.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.052932 restraints weight = 37654.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.054446 restraints weight = 24542.279| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9671 Z= 0.208 Angle : 0.632 13.354 13103 Z= 0.340 Chirality : 0.041 0.148 1454 Planarity : 0.005 0.133 1703 Dihedral : 11.181 178.252 1350 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 35.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.52 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1193 helix: 1.59 (0.23), residues: 529 sheet: -0.11 (0.36), residues: 221 loop : -0.45 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 21 HIS 0.008 0.002 HIS H 139 PHE 0.023 0.002 PHE K 293 TYR 0.017 0.001 TYR K 75 ARG 0.018 0.001 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.04949 ( 481) hydrogen bonds : angle 5.30390 ( 1461) covalent geometry : bond 0.00410 ( 9667) covalent geometry : angle 0.63250 (13103) Misc. bond : bond 0.00226 ( 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 134 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.361 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: A 76 ASP cc_start: 0.8602 (t0) cc_final: 0.8380 (t0) REVERT: A 267 PHE cc_start: 0.8927 (m-80) cc_final: 0.8685 (m-10) REVERT: A 302 MET cc_start: 0.9317 (mmp) cc_final: 0.9110 (mmt) REVERT: A 317 LEU cc_start: 0.9037 (mm) cc_final: 0.8765 (mp) REVERT: A 351 PHE cc_start: 0.7796 (m-80) cc_final: 0.7025 (m-80) REVERT: H 37 HIS cc_start: 0.8621 (m-70) cc_final: 0.8353 (m-70) REVERT: H 181 VAL cc_start: 0.8903 (t) cc_final: 0.8693 (p) REVERT: H 325 MET cc_start: 0.8368 (mmt) cc_final: 0.7826 (mmm) REVERT: H 372 LYS cc_start: 0.8840 (mptt) cc_final: 0.8535 (mmtm) REVERT: K 6 MET cc_start: 0.5668 (tpp) cc_final: 0.5327 (tpp) REVERT: K 144 PHE cc_start: 0.9009 (t80) cc_final: 0.8227 (t80) REVERT: K 190 MET cc_start: 0.9263 (tmm) cc_final: 0.8729 (tmm) REVERT: K 215 HIS cc_start: 0.9133 (m-70) cc_final: 0.8862 (m-70) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2900 time to fit residues: 55.5877 Evaluate side-chains 104 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 108 optimal weight: 40.0000 chunk 69 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** 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 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.070754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050464 restraints weight = 70709.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.052767 restraints weight = 36710.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.054263 restraints weight = 23621.138| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9671 Z= 0.148 Angle : 0.525 6.266 13103 Z= 0.284 Chirality : 0.041 0.259 1454 Planarity : 0.010 0.409 1703 Dihedral : 10.866 179.231 1350 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 36.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1193 helix: 1.78 (0.23), residues: 528 sheet: -0.22 (0.36), residues: 214 loop : -0.36 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 21 HIS 0.009 0.001 HIS H 139 PHE 0.013 0.001 PHE H 262 TYR 0.014 0.001 TYR K 75 ARG 0.008 0.000 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 481) hydrogen bonds : angle 5.12858 ( 1461) covalent geometry : bond 0.00294 ( 9667) covalent geometry : angle 0.52503 (13103) Misc. bond : bond 0.00329 ( 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 142 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 2.936 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: A 267 PHE cc_start: 0.8936 (m-80) cc_final: 0.8640 (m-10) REVERT: A 302 MET cc_start: 0.9330 (mmp) cc_final: 0.9003 (mmt) REVERT: A 317 LEU cc_start: 0.9086 (mm) cc_final: 0.8858 (mp) REVERT: A 351 PHE cc_start: 0.7837 (m-80) cc_final: 0.7140 (m-80) REVERT: H 37 HIS cc_start: 0.8576 (m-70) cc_final: 0.8321 (m-70) REVERT: H 325 MET cc_start: 0.8243 (mmt) cc_final: 0.7519 (mmm) REVERT: H 372 LYS cc_start: 0.8845 (mptt) cc_final: 0.8569 (mmtm) REVERT: K 144 PHE cc_start: 0.8994 (t80) cc_final: 0.8252 (t80) REVERT: K 215 HIS cc_start: 0.9115 (m-70) cc_final: 0.8233 (m-70) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.3789 time to fit residues: 79.3506 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 : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 109 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 26 optimal weight: 30.0000 chunk 27 optimal weight: 0.4980 chunk 100 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 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** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.068447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048161 restraints weight = 72019.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050301 restraints weight = 38010.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.051703 restraints weight = 24675.948| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9671 Z= 0.180 Angle : 0.551 7.020 13103 Z= 0.293 Chirality : 0.040 0.212 1454 Planarity : 0.010 0.376 1703 Dihedral : 10.853 178.361 1350 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 40.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1193 helix: 1.76 (0.23), residues: 533 sheet: -0.35 (0.36), residues: 201 loop : -0.34 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 407 HIS 0.006 0.001 HIS H 139 PHE 0.015 0.002 PHE K 144 TYR 0.014 0.001 TYR K 75 ARG 0.004 0.000 ARG H 308 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 481) hydrogen bonds : angle 5.01144 ( 1461) covalent geometry : bond 0.00359 ( 9667) covalent geometry : angle 0.55118 (13103) Misc. bond : bond 0.00332 ( 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 : 1.199 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: A 76 ASP cc_start: 0.9093 (t70) cc_final: 0.8566 (t0) REVERT: A 118 VAL cc_start: 0.9584 (m) cc_final: 0.9297 (p) REVERT: A 267 PHE cc_start: 0.9026 (m-80) cc_final: 0.8654 (m-10) REVERT: A 302 MET cc_start: 0.9469 (mmp) cc_final: 0.8852 (mpp) REVERT: H 37 HIS cc_start: 0.8778 (m-70) cc_final: 0.8474 (m-70) REVERT: H 50 ASN cc_start: 0.8737 (p0) cc_final: 0.8399 (p0) REVERT: H 389 LYS cc_start: 0.9517 (ttmt) cc_final: 0.9297 (mtmm) REVERT: K 144 PHE cc_start: 0.9053 (t80) cc_final: 0.8291 (t80) REVERT: K 190 MET cc_start: 0.9432 (ppp) cc_final: 0.9145 (ppp) REVERT: K 215 HIS cc_start: 0.9195 (m-70) cc_final: 0.8097 (m-70) REVERT: K 293 PHE cc_start: 0.6660 (t80) cc_final: 0.6421 (t80) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3101 time to fit residues: 54.5894 Evaluate side-chains 97 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 55 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** 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 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** ** K 52 ASN ** 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 = 0.3588 r_free = 0.3588 target = 0.066553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.046527 restraints weight = 74052.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.048607 restraints weight = 38591.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.049962 restraints weight = 24851.298| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9671 Z= 0.220 Angle : 0.584 6.642 13103 Z= 0.314 Chirality : 0.040 0.143 1454 Planarity : 0.009 0.353 1703 Dihedral : 11.129 174.719 1350 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 48.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1193 helix: 1.47 (0.23), residues: 529 sheet: -0.62 (0.36), residues: 210 loop : -0.55 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 407 HIS 0.006 0.002 HIS A 139 PHE 0.020 0.002 PHE H 169 TYR 0.020 0.002 TYR A 224 ARG 0.006 0.001 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 481) hydrogen bonds : angle 5.16515 ( 1461) covalent geometry : bond 0.00429 ( 9667) covalent geometry : angle 0.58359 (13103) Misc. bond : bond 0.00285 ( 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 117 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.389 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: 0.9492 (t) cc_final: 0.9252 (p) REVERT: A 76 ASP cc_start: 0.9015 (t70) cc_final: 0.8547 (t0) REVERT: A 118 VAL cc_start: 0.9607 (m) cc_final: 0.9299 (p) REVERT: A 267 PHE cc_start: 0.9005 (m-80) cc_final: 0.8574 (m-10) REVERT: A 302 MET cc_start: 0.9482 (mmp) cc_final: 0.8903 (mpp) REVERT: H 50 ASN cc_start: 0.8747 (p0) cc_final: 0.8523 (p0) REVERT: H 295 MET cc_start: 0.8758 (ttm) cc_final: 0.8440 (ttm) REVERT: H 325 MET cc_start: 0.8793 (mmp) cc_final: 0.8068 (tpp) REVERT: H 389 LYS cc_start: 0.9499 (ttmt) cc_final: 0.9245 (mtmm) REVERT: H 413 MET cc_start: 0.7628 (mmt) cc_final: 0.7022 (mmp) REVERT: K 144 PHE cc_start: 0.9071 (t80) cc_final: 0.8432 (t80) REVERT: K 215 HIS cc_start: 0.9313 (m-70) cc_final: 0.8036 (m-70) REVERT: K 293 PHE cc_start: 0.6951 (t80) cc_final: 0.6669 (t80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2962 time to fit residues: 50.2821 Evaluate side-chains 96 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** 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 193 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.067524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.047626 restraints weight = 71559.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.049747 restraints weight = 37137.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.051140 restraints weight = 23838.492| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.6480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9671 Z= 0.121 Angle : 0.475 6.637 13103 Z= 0.253 Chirality : 0.039 0.141 1454 Planarity : 0.009 0.334 1703 Dihedral : 11.050 178.541 1350 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 43.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1193 helix: 1.85 (0.23), residues: 531 sheet: -0.64 (0.36), residues: 209 loop : -0.43 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS H 37 PHE 0.012 0.001 PHE K 144 TYR 0.012 0.001 TYR K 75 ARG 0.004 0.000 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 481) hydrogen bonds : angle 4.83983 ( 1461) covalent geometry : bond 0.00243 ( 9667) covalent geometry : angle 0.47499 (13103) Misc. bond : bond 0.00275 ( 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 118 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.301 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: A 14 VAL cc_start: 0.9459 (t) cc_final: 0.9220 (p) REVERT: A 76 ASP cc_start: 0.9091 (t70) cc_final: 0.8580 (t0) REVERT: A 118 VAL cc_start: 0.9597 (m) cc_final: 0.9262 (p) REVERT: A 230 LEU cc_start: 0.9562 (tt) cc_final: 0.9322 (mm) REVERT: A 267 PHE cc_start: 0.9013 (m-80) cc_final: 0.8547 (m-10) REVERT: A 302 MET cc_start: 0.9454 (mmp) cc_final: 0.8737 (mpp) REVERT: H 275 LEU cc_start: 0.9271 (mt) cc_final: 0.9017 (mp) REVERT: H 295 MET cc_start: 0.8593 (ttm) cc_final: 0.8369 (ttm) REVERT: H 301 MET cc_start: 0.8510 (mmp) cc_final: 0.8270 (mmp) REVERT: H 302 MET cc_start: 0.7763 (mpp) cc_final: 0.7462 (mpp) REVERT: H 389 LYS cc_start: 0.9496 (ttmt) cc_final: 0.9245 (mtmm) REVERT: H 413 MET cc_start: 0.7759 (mmt) cc_final: 0.7176 (mmp) REVERT: K 144 PHE cc_start: 0.9051 (t80) cc_final: 0.8355 (t80) REVERT: K 153 CYS cc_start: 0.9049 (t) cc_final: 0.8672 (m) REVERT: K 190 MET cc_start: 0.9406 (ppp) cc_final: 0.9152 (ppp) REVERT: K 215 HIS cc_start: 0.9245 (m-70) cc_final: 0.8172 (m-70) REVERT: K 293 PHE cc_start: 0.7039 (t80) cc_final: 0.6775 (t80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2744 time to fit residues: 46.5132 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 : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 42 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 93 optimal weight: 40.0000 chunk 58 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.067453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.047440 restraints weight = 72361.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.049679 restraints weight = 36166.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.051146 restraints weight = 22752.532| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9671 Z= 0.114 Angle : 0.464 6.383 13103 Z= 0.245 Chirality : 0.039 0.139 1454 Planarity : 0.008 0.315 1703 Dihedral : 10.951 179.646 1350 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 43.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1193 helix: 2.06 (0.23), residues: 525 sheet: -0.58 (0.36), residues: 209 loop : -0.35 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.002 0.001 HIS H 139 PHE 0.011 0.001 PHE K 144 TYR 0.012 0.001 TYR K 75 ARG 0.004 0.000 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 481) hydrogen bonds : angle 4.74839 ( 1461) covalent geometry : bond 0.00231 ( 9667) covalent geometry : angle 0.46352 (13103) Misc. bond : bond 0.00270 ( 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 122 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.178 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: A 76 ASP cc_start: 0.9005 (t70) cc_final: 0.8485 (t0) REVERT: A 109 THR cc_start: 0.9113 (m) cc_final: 0.8814 (p) REVERT: A 118 VAL cc_start: 0.9561 (m) cc_final: 0.9236 (p) REVERT: A 230 LEU cc_start: 0.9546 (tt) cc_final: 0.9304 (mm) REVERT: A 267 PHE cc_start: 0.8948 (m-80) cc_final: 0.8474 (m-10) REVERT: A 302 MET cc_start: 0.9444 (mmp) cc_final: 0.8775 (mpp) REVERT: H 295 MET cc_start: 0.8477 (ttm) cc_final: 0.8224 (ttm) REVERT: H 325 MET cc_start: 0.7740 (mpp) cc_final: 0.7394 (mpp) REVERT: H 389 LYS cc_start: 0.9477 (ttmt) cc_final: 0.9216 (mtmm) REVERT: H 413 MET cc_start: 0.7924 (mmt) cc_final: 0.6848 (mmt) REVERT: K 144 PHE cc_start: 0.8997 (t80) cc_final: 0.8303 (t80) REVERT: K 153 CYS cc_start: 0.9005 (t) cc_final: 0.8635 (m) REVERT: K 190 MET cc_start: 0.9387 (ppp) cc_final: 0.9139 (ppp) REVERT: K 215 HIS cc_start: 0.9248 (m-70) cc_final: 0.8108 (m-70) REVERT: K 261 MET cc_start: 0.9039 (mtp) cc_final: 0.8824 (mtp) REVERT: K 293 PHE cc_start: 0.6979 (t80) cc_final: 0.6762 (t80) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2625 time to fit residues: 46.0614 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 : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 20.0000 chunk 21 optimal weight: 0.0370 chunk 0 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 overall best weight: 2.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** 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 ** 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** 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 = 0.067971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.047967 restraints weight = 71742.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050122 restraints weight = 36973.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.051502 restraints weight = 23660.296| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.6707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9671 Z= 0.113 Angle : 0.461 6.061 13103 Z= 0.245 Chirality : 0.039 0.139 1454 Planarity : 0.012 0.463 1703 Dihedral : 10.463 176.853 1350 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 42.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1193 helix: 2.09 (0.23), residues: 525 sheet: -0.56 (0.36), residues: 209 loop : -0.30 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.002 0.001 HIS H 139 PHE 0.035 0.001 PHE K 293 TYR 0.012 0.001 TYR K 75 ARG 0.005 0.000 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 481) hydrogen bonds : angle 4.72834 ( 1461) covalent geometry : bond 0.00229 ( 9667) covalent geometry : angle 0.46086 (13103) Misc. bond : bond 0.00295 ( 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 121 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.269 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: A 76 ASP cc_start: 0.9046 (t70) cc_final: 0.8506 (t0) REVERT: A 109 THR cc_start: 0.9036 (m) cc_final: 0.8713 (p) REVERT: A 118 VAL cc_start: 0.9569 (m) cc_final: 0.9262 (p) REVERT: A 267 PHE cc_start: 0.8970 (m-80) cc_final: 0.8521 (m-10) REVERT: A 302 MET cc_start: 0.9441 (mmp) cc_final: 0.8869 (mpp) REVERT: H 295 MET cc_start: 0.8569 (ttm) cc_final: 0.8326 (ttm) REVERT: H 325 MET cc_start: 0.7670 (mpp) cc_final: 0.7338 (mpp) REVERT: H 372 LYS cc_start: 0.9006 (mptt) cc_final: 0.8741 (mmtm) REVERT: H 389 LYS cc_start: 0.9514 (ttmt) cc_final: 0.9299 (mtmm) REVERT: H 413 MET cc_start: 0.7896 (mmt) cc_final: 0.6872 (mmt) REVERT: K 144 PHE cc_start: 0.9049 (t80) cc_final: 0.8345 (t80) REVERT: K 153 CYS cc_start: 0.9054 (t) cc_final: 0.8675 (m) REVERT: K 215 HIS cc_start: 0.9291 (m-70) cc_final: 0.8123 (m-70) REVERT: K 261 MET cc_start: 0.9018 (mtp) cc_final: 0.8815 (mtp) REVERT: K 293 PHE cc_start: 0.6347 (t80) cc_final: 0.6045 (t80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2932 time to fit residues: 50.9442 Evaluate side-chains 99 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 50 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 102 optimal weight: 30.0000 chunk 33 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.066486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.046518 restraints weight = 72441.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048573 restraints weight = 38026.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049915 restraints weight = 24668.702| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9671 Z= 0.211 Angle : 0.553 6.577 13103 Z= 0.295 Chirality : 0.039 0.143 1454 Planarity : 0.012 0.462 1703 Dihedral : 10.402 176.055 1350 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 49.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1193 helix: 1.71 (0.23), residues: 525 sheet: -0.71 (0.36), residues: 205 loop : -0.46 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 388 HIS 0.004 0.001 HIS A 28 PHE 0.017 0.002 PHE K 293 TYR 0.013 0.002 TYR H 432 ARG 0.008 0.001 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 481) hydrogen bonds : angle 4.98188 ( 1461) covalent geometry : bond 0.00413 ( 9667) covalent geometry : angle 0.55346 (13103) Misc. bond : bond 0.00297 ( 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 114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.204 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 71 GLU cc_start: 0.6778 (mp0) cc_final: 0.6269 (mp0) REVERT: A 76 ASP cc_start: 0.9107 (t70) cc_final: 0.8615 (t0) REVERT: A 118 VAL cc_start: 0.9575 (m) cc_final: 0.9271 (p) REVERT: A 267 PHE cc_start: 0.9039 (m-80) cc_final: 0.8637 (m-10) REVERT: A 302 MET cc_start: 0.9464 (mmp) cc_final: 0.8791 (mpp) REVERT: H 290 GLU cc_start: 0.8052 (tp30) cc_final: 0.7783 (tp30) REVERT: H 295 MET cc_start: 0.8590 (ttm) cc_final: 0.8343 (ttm) REVERT: H 325 MET cc_start: 0.7853 (mpp) cc_final: 0.7538 (mpp) REVERT: H 389 LYS cc_start: 0.9487 (ttmt) cc_final: 0.9207 (mtmm) REVERT: H 413 MET cc_start: 0.7707 (mmt) cc_final: 0.6692 (mmt) REVERT: K 144 PHE cc_start: 0.9071 (t80) cc_final: 0.8390 (t80) REVERT: K 153 CYS cc_start: 0.9051 (t) cc_final: 0.8699 (m) REVERT: K 215 HIS cc_start: 0.9342 (m-70) cc_final: 0.8192 (m-70) REVERT: K 293 PHE cc_start: 0.6899 (t80) cc_final: 0.6464 (t80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2752 time to fit residues: 45.1922 Evaluate side-chains 91 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 84 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 4 optimal weight: 0.2980 overall best weight: 7.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** 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 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** K 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.065927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046229 restraints weight = 71563.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048320 restraints weight = 36307.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.049710 restraints weight = 23106.496| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.7265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9671 Z= 0.192 Angle : 0.535 7.053 13103 Z= 0.287 Chirality : 0.040 0.179 1454 Planarity : 0.010 0.365 1703 Dihedral : 10.181 170.220 1350 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 49.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1193 helix: 1.61 (0.23), residues: 525 sheet: -0.97 (0.37), residues: 194 loop : -0.57 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 388 HIS 0.006 0.001 HIS A 139 PHE 0.023 0.002 PHE H 135 TYR 0.012 0.001 TYR K 75 ARG 0.021 0.001 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 481) hydrogen bonds : angle 5.02675 ( 1461) covalent geometry : bond 0.00379 ( 9667) covalent geometry : angle 0.53526 (13103) Misc. bond : bond 0.00333 ( 4) =============================================================================== Job complete usr+sys time: 3696.60 seconds wall clock time: 66 minutes 29.52 seconds (3989.52 seconds total)