Starting phenix.real_space_refine on Tue Nov 18 09:49:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q2n_20575/11_2025/6q2n_20575_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q2n_20575/11_2025/6q2n_20575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6q2n_20575/11_2025/6q2n_20575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q2n_20575/11_2025/6q2n_20575.map" model { file = "/net/cci-nas-00/data/ceres_data/6q2n_20575/11_2025/6q2n_20575_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q2n_20575/11_2025/6q2n_20575_neut.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 116 5.16 5 C 8228 2.51 5 N 2302 2.21 5 O 2486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13140 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 659 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1554 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 192} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 4353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4353 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 518} Chain breaks: 8 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, D, F Time building chain proxies: 4.19, per 1000 atoms: 0.32 Number of scatterers: 13140 At special positions: 0 Unit cell: (127.33, 210.79, 75.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 116 16.00 O 2486 8.00 N 2302 7.00 C 8228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 179 " distance=2.02 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 208 " distance=2.02 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS A 210 " distance=2.04 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS B 178 " distance=2.10 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 167 " distance=2.04 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 192 " distance=2.01 Simple disulfide: pdb=" SG CYS C 187 " - pdb=" SG CYS C 233 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 221 " distance=2.03 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 313 " distance=2.03 Simple disulfide: pdb=" SG CYS C 250 " - pdb=" SG CYS C 256 " distance=2.04 Simple disulfide: pdb=" SG CYS C 267 " - pdb=" SG CYS C 285 " distance=2.03 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 325 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 142 " distance=2.02 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 243 " distance=2.02 Simple disulfide: pdb=" SG CYS E 426 " - pdb=" SG CYS E 430 " distance=2.03 Simple disulfide: pdb=" SG CYS E 449 " - pdb=" SG CYS E 478 " distance=2.04 Simple disulfide: pdb=" SG CYS E 515 " - pdb=" SG CYS E 531 " distance=2.02 Simple disulfide: pdb=" SG CYS E 519 " - pdb=" SG CYS E 541 " distance=2.03 Simple disulfide: pdb=" SG CYS E 528 " - pdb=" SG CYS E 558 " distance=2.02 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 581 " distance=2.01 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 609 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 611 " - pdb=" SG CYS E 618 " distance=2.01 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 179 " distance=2.02 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 208 " distance=2.02 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 210 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 167 " distance=2.04 Simple disulfide: pdb=" SG CYS D 178 " - pdb=" SG CYS D 192 " distance=2.01 Simple disulfide: pdb=" SG CYS D 187 " - pdb=" SG CYS D 233 " distance=2.03 Simple disulfide: pdb=" SG CYS D 216 " - pdb=" SG CYS D 221 " distance=2.04 Simple disulfide: pdb=" SG CYS D 243 " - pdb=" SG CYS D 313 " distance=2.03 Simple disulfide: pdb=" SG CYS D 250 " - pdb=" SG CYS D 256 " distance=2.03 Simple disulfide: pdb=" SG CYS D 267 " - pdb=" SG CYS D 285 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 315 " - pdb=" SG CYS D 325 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 142 " distance=2.02 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 243 " distance=2.02 Simple disulfide: pdb=" SG CYS F 426 " - pdb=" SG CYS F 430 " distance=2.03 Simple disulfide: pdb=" SG CYS F 449 " - pdb=" SG CYS F 478 " distance=2.04 Simple disulfide: pdb=" SG CYS F 515 " - pdb=" SG CYS F 531 " distance=2.02 Simple disulfide: pdb=" SG CYS F 519 " - pdb=" SG CYS F 541 " distance=2.03 Simple disulfide: pdb=" SG CYS F 528 " - pdb=" SG CYS F 558 " distance=2.02 Simple disulfide: pdb=" SG CYS F 565 " - pdb=" SG CYS F 581 " distance=2.01 Simple disulfide: pdb=" SG CYS F 570 " - pdb=" SG CYS F 585 " distance=2.03 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS F 620 " distance=2.03 Simple disulfide: pdb=" SG CYS F 611 " - pdb=" SG CYS F 618 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 571.5 milliseconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 36 sheets defined 24.3% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'C' and resid 152 through 164 removed outlier: 3.649A pdb=" N ASP C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.516A pdb=" N CYS C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 4.199A pdb=" N SER C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 227 removed outlier: 3.533A pdb=" N THR C 222 " --> pdb=" O ASP C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 235 Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.724A pdb=" N CYS C 267 " --> pdb=" O PHE C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 290 Processing helix chain 'C' and resid 321 through 334 removed outlier: 3.923A pdb=" N PHE C 331 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 332 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 Processing helix chain 'E' and resid 102 through 111 removed outlier: 3.766A pdb=" N VAL E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 160 removed outlier: 3.746A pdb=" N LEU E 160 " --> pdb=" O CYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 167 removed outlier: 4.025A pdb=" N CYS E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 162 through 167' Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 309 through 314 removed outlier: 3.787A pdb=" N ARG E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.785A pdb=" N ALA E 432 " --> pdb=" O ASN E 429 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE E 433 " --> pdb=" O CYS E 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 429 through 433' Processing helix chain 'E' and resid 524 through 530 Processing helix chain 'E' and resid 564 through 568 removed outlier: 4.213A pdb=" N ASP E 567 " --> pdb=" O THR E 564 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY E 568 " --> pdb=" O CYS E 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 564 through 568' Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.650A pdb=" N ASP D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 188 through 203 removed outlier: 3.515A pdb=" N CYS D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 removed outlier: 4.198A pdb=" N SER D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 227 removed outlier: 3.533A pdb=" N THR D 222 " --> pdb=" O ASP D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 235 Processing helix chain 'D' and resid 242 through 252 Processing helix chain 'D' and resid 253 through 267 removed outlier: 3.725A pdb=" N CYS D 267 " --> pdb=" O PHE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 290 Processing helix chain 'D' and resid 321 through 334 removed outlier: 3.924A pdb=" N PHE D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 Processing helix chain 'F' and resid 102 through 111 removed outlier: 3.767A pdb=" N VAL F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 160 removed outlier: 3.746A pdb=" N LEU F 160 " --> pdb=" O CYS F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 4.024A pdb=" N CYS F 166 " --> pdb=" O PRO F 162 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 162 through 167' Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.788A pdb=" N ARG F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.785A pdb=" N ALA F 432 " --> pdb=" O ASN F 429 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE F 433 " --> pdb=" O CYS F 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 429 through 433' Processing helix chain 'F' and resid 524 through 530 Processing helix chain 'F' and resid 564 through 568 removed outlier: 4.213A pdb=" N ASP F 567 " --> pdb=" O THR F 564 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY F 568 " --> pdb=" O CYS F 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 564 through 568' Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 126 Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA4, first strand: chain 'C' and resid 300 through 301 Processing sheet with id=AA5, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.383A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 39 through 42 removed outlier: 4.644A pdb=" N VAL E 42 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N THR E 152 " --> pdb=" O VAL E 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 71 through 73 removed outlier: 4.249A pdb=" N HIS E 81 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'E' and resid 174 through 176 removed outlier: 3.508A pdb=" N VAL E 256 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E 241 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR E 237 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.035A pdb=" N THR E 184 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR E 225 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N HIS E 186 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 280 through 283 removed outlier: 3.711A pdb=" N ALA E 281 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER E 396 " --> pdb=" O ALA E 281 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA E 373 " --> pdb=" O LEU E 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 292 through 298 removed outlier: 6.296A pdb=" N LEU E 356 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR E 295 " --> pdb=" O TYR E 354 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR E 354 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG E 297 " --> pdb=" O HIS E 352 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS E 352 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP E 353 " --> pdb=" O TRP E 334 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP E 334 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 407 through 412 removed outlier: 6.870A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU E 410 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS E 482 " --> pdb=" O SER E 445 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 424 through 425 removed outlier: 3.760A pdb=" N SER E 462 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE E 464 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL E 455 " --> pdb=" O ILE E 464 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 542 through 544 Processing sheet with id=AB8, first strand: chain 'E' and resid 594 through 596 Processing sheet with id=AB9, first strand: chain 'E' and resid 608 through 612 Processing sheet with id=AC1, first strand: chain 'B' and resid 119 through 126 Processing sheet with id=AC2, first strand: chain 'B' and resid 180 through 181 Processing sheet with id=AC3, first strand: chain 'B' and resid 190 through 191 Processing sheet with id=AC4, first strand: chain 'D' and resid 300 through 301 Processing sheet with id=AC5, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AC6, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.381A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 39 through 42 removed outlier: 4.643A pdb=" N VAL F 42 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N THR F 152 " --> pdb=" O VAL F 42 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 71 through 73 removed outlier: 6.699A pdb=" N LEU F 72 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 86 through 89 Processing sheet with id=AD1, first strand: chain 'F' and resid 174 through 176 removed outlier: 3.508A pdb=" N VAL F 256 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR F 237 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.035A pdb=" N THR F 184 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR F 225 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N HIS F 186 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 280 through 283 removed outlier: 3.711A pdb=" N ALA F 281 " --> pdb=" O ASN F 394 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER F 396 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA F 373 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 292 through 298 removed outlier: 6.296A pdb=" N LEU F 356 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR F 295 " --> pdb=" O TYR F 354 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR F 354 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG F 297 " --> pdb=" O HIS F 352 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS F 352 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP F 353 " --> pdb=" O TRP F 334 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP F 334 " --> pdb=" O ASP F 353 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 407 through 412 removed outlier: 6.870A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU F 410 " --> pdb=" O THR F 503 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS F 482 " --> pdb=" O SER F 445 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 424 through 425 removed outlier: 3.760A pdb=" N SER F 462 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE F 464 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL F 455 " --> pdb=" O ILE F 464 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AD8, first strand: chain 'F' and resid 594 through 596 Processing sheet with id=AD9, first strand: chain 'F' and resid 608 through 612 402 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4351 1.34 - 1.47: 3239 1.47 - 1.60: 5690 1.60 - 1.72: 0 1.72 - 1.85: 126 Bond restraints: 13406 Sorted by residual: bond pdb=" CA ASN F 113 " pdb=" C ASN F 113 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.34e-02 5.57e+03 1.41e+01 bond pdb=" CA ASN E 113 " pdb=" C ASN E 113 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.34e-02 5.57e+03 1.38e+01 bond pdb=" C THR C 298 " pdb=" N PRO C 299 " ideal model delta sigma weight residual 1.329 1.294 0.036 1.25e-02 6.40e+03 8.21e+00 bond pdb=" C THR D 298 " pdb=" N PRO D 299 " ideal model delta sigma weight residual 1.329 1.294 0.035 1.25e-02 6.40e+03 7.81e+00 bond pdb=" C GLN F 583 " pdb=" N ASP F 584 " ideal model delta sigma weight residual 1.333 1.295 0.038 1.47e-02 4.63e+03 6.63e+00 ... (remaining 13401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 17952 4.14 - 8.28: 208 8.28 - 12.42: 8 12.42 - 16.56: 2 16.56 - 20.70: 2 Bond angle restraints: 18172 Sorted by residual: angle pdb=" C ARG E 112 " pdb=" N ASN E 113 " pdb=" CA ASN E 113 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C ARG F 112 " pdb=" N ASN F 113 " pdb=" CA ASN F 113 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C TYR F 76 " pdb=" N ARG F 77 " pdb=" CA ARG F 77 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C TYR E 76 " pdb=" N ARG E 77 " pdb=" CA ARG E 77 " ideal model delta sigma weight residual 121.54 129.62 -8.08 1.91e+00 2.74e-01 1.79e+01 angle pdb=" N GLU A 153 " pdb=" CA GLU A 153 " pdb=" C GLU A 153 " ideal model delta sigma weight residual 110.80 119.10 -8.30 2.13e+00 2.20e-01 1.52e+01 ... (remaining 18167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7826 17.65 - 35.30: 347 35.30 - 52.94: 43 52.94 - 70.59: 0 70.59 - 88.24: 9 Dihedral angle restraints: 8225 sinusoidal: 3335 harmonic: 4890 Sorted by residual: dihedral pdb=" CB CYS A 178 " pdb=" SG CYS A 178 " pdb=" SG CYS B 178 " pdb=" CB CYS B 178 " ideal model delta sinusoidal sigma weight residual 93.00 -178.76 -88.24 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CB CYS F 515 " pdb=" SG CYS F 515 " pdb=" SG CYS F 531 " pdb=" CB CYS F 531 " ideal model delta sinusoidal sigma weight residual 93.00 172.88 -79.88 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS E 515 " pdb=" SG CYS E 515 " pdb=" SG CYS E 531 " pdb=" CB CYS E 531 " ideal model delta sinusoidal sigma weight residual 93.00 172.87 -79.87 1 1.00e+01 1.00e-02 7.91e+01 ... (remaining 8222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1407 0.060 - 0.120: 493 0.120 - 0.180: 119 0.180 - 0.240: 11 0.240 - 0.300: 4 Chirality restraints: 2034 Sorted by residual: chirality pdb=" CA GLU B 153 " pdb=" N GLU B 153 " pdb=" C GLU B 153 " pdb=" CB GLU B 153 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA GLU A 153 " pdb=" N GLU A 153 " pdb=" C GLU A 153 " pdb=" CB GLU A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CG LEU D 155 " pdb=" CB LEU D 155 " pdb=" CD1 LEU D 155 " pdb=" CD2 LEU D 155 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2031 not shown) Planarity restraints: 2362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 230 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.15e+00 pdb=" C VAL C 230 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL C 230 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO C 231 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 230 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.04e+00 pdb=" C VAL D 230 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL D 230 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO D 231 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 286 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.84e+00 pdb=" C LEU C 286 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU C 286 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU C 287 " 0.015 2.00e-02 2.50e+03 ... (remaining 2359 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 18 2.14 - 2.83: 4093 2.83 - 3.52: 16799 3.52 - 4.21: 30146 4.21 - 4.90: 49236 Nonbonded interactions: 100292 Sorted by model distance: nonbonded pdb=" OD1 ASP E 567 " pdb=" OD2 ASP E 584 " model vdw 1.449 3.040 nonbonded pdb=" OD1 ASP F 567 " pdb=" OD2 ASP F 584 " model vdw 1.449 3.040 nonbonded pdb=" OD2 ASP E 300 " pdb=" OD2 ASP E 378 " model vdw 1.490 3.040 nonbonded pdb=" OD2 ASP F 300 " pdb=" OD2 ASP F 378 " model vdw 1.491 3.040 nonbonded pdb=" OD1 ASP F 266 " pdb=" OD2 ASP F 302 " model vdw 1.605 3.040 ... (remaining 100287 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.690 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5557 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 : 0.008 0.082 13457 Z= 0.358 Angle : 1.246 20.703 18274 Z= 0.691 Chirality : 0.063 0.300 2034 Planarity : 0.008 0.059 2362 Dihedral : 9.781 78.043 4896 Min Nonbonded Distance : 1.449 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.57 % Favored : 90.18 % Rotamer: Outliers : 0.68 % Allowed : 2.30 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.17), residues: 1630 helix: -3.05 (0.19), residues: 326 sheet: -2.08 (0.26), residues: 376 loop : -3.16 (0.17), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG C 171 TYR 0.028 0.005 TYR D 174 PHE 0.026 0.004 PHE B 142 TRP 0.037 0.004 TRP F 139 HIS 0.010 0.002 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00754 (13406) covalent geometry : angle 1.23657 (18172) SS BOND : bond 0.01323 ( 51) SS BOND : angle 2.40865 ( 102) hydrogen bonds : bond 0.20264 ( 402) hydrogen bonds : angle 9.25248 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 311 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PRO cc_start: 0.7509 (Cg_endo) cc_final: 0.7264 (Cg_exo) REVERT: E 73 TYR cc_start: 0.6775 (m-10) cc_final: 0.5407 (m-10) REVERT: E 122 TYR cc_start: 0.5348 (p90) cc_final: 0.5007 (p90) REVERT: E 153 SER cc_start: 0.8798 (m) cc_final: 0.8356 (t) REVERT: D 200 PHE cc_start: 0.7511 (m-80) cc_final: 0.6561 (m-80) REVERT: F 73 TYR cc_start: 0.6790 (m-10) cc_final: 0.5396 (m-10) REVERT: F 122 TYR cc_start: 0.5410 (p90) cc_final: 0.4955 (p90) REVERT: F 136 GLU cc_start: 0.2480 (tt0) cc_final: 0.2221 (mm-30) REVERT: F 153 SER cc_start: 0.8827 (m) cc_final: 0.8397 (t) REVERT: F 357 VAL cc_start: 0.7855 (t) cc_final: 0.7649 (p) outliers start: 10 outliers final: 6 residues processed: 320 average time/residue: 0.1343 time to fit residues: 59.1755 Evaluate side-chains 154 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.4980 overall best weight: 2.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN E 81 HIS ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN E 246 HIS ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 ASN E 392 HIS E 403 HIS E 443 HIS B 176 GLN D 162 ASN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN F 81 HIS ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN F 246 HIS ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN F 392 HIS F 403 HIS F 443 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.163721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.145691 restraints weight = 48767.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.148827 restraints weight = 34884.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.148947 restraints weight = 23012.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.149712 restraints weight = 22338.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.149766 restraints weight = 19157.655| |-----------------------------------------------------------------------------| r_work (final): 0.4431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5565 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13457 Z= 0.144 Angle : 0.770 10.280 18274 Z= 0.396 Chirality : 0.046 0.160 2034 Planarity : 0.006 0.051 2362 Dihedral : 6.811 28.391 1822 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.41 % Allowed : 3.25 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.18), residues: 1630 helix: -1.59 (0.25), residues: 312 sheet: -1.76 (0.27), residues: 366 loop : -2.83 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 544 TYR 0.023 0.002 TYR C 301 PHE 0.018 0.002 PHE C 331 TRP 0.013 0.002 TRP F 139 HIS 0.008 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00309 (13406) covalent geometry : angle 0.76468 (18172) SS BOND : bond 0.00481 ( 51) SS BOND : angle 1.42091 ( 102) hydrogen bonds : bond 0.04431 ( 402) hydrogen bonds : angle 6.79766 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 215 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PRO cc_start: 0.7696 (Cg_endo) cc_final: 0.7443 (Cg_exo) REVERT: E 73 TYR cc_start: 0.6406 (m-10) cc_final: 0.5376 (m-10) REVERT: E 289 GLU cc_start: 0.8539 (tp30) cc_final: 0.8021 (tp30) REVERT: E 290 ASP cc_start: 0.7201 (m-30) cc_final: 0.6924 (m-30) REVERT: E 617 LYS cc_start: 0.7099 (ttmt) cc_final: 0.6371 (mttp) REVERT: B 125 LEU cc_start: 0.6437 (mt) cc_final: 0.6215 (mt) REVERT: B 178 CYS cc_start: 0.2487 (OUTLIER) cc_final: 0.2280 (t) REVERT: D 200 PHE cc_start: 0.7010 (m-80) cc_final: 0.6673 (m-80) REVERT: F 73 TYR cc_start: 0.6536 (m-10) cc_final: 0.5298 (m-10) REVERT: F 289 GLU cc_start: 0.8513 (tp30) cc_final: 0.7990 (tp30) REVERT: F 290 ASP cc_start: 0.7155 (m-30) cc_final: 0.6873 (m-30) REVERT: F 466 PHE cc_start: 0.5149 (p90) cc_final: 0.4948 (p90) REVERT: F 617 LYS cc_start: 0.7104 (ttmt) cc_final: 0.6356 (mttp) outliers start: 6 outliers final: 2 residues processed: 221 average time/residue: 0.1205 time to fit residues: 37.6861 Evaluate side-chains 138 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 117 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 11 optimal weight: 0.0770 chunk 48 optimal weight: 50.0000 chunk 129 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 overall best weight: 5.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN E 187 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 HIS B 124 HIS D 253 ASN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.156246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.137263 restraints weight = 46679.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.138510 restraints weight = 35593.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.139462 restraints weight = 28651.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.140621 restraints weight = 22926.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.140921 restraints weight = 19970.166| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 13457 Z= 0.251 Angle : 0.893 10.762 18274 Z= 0.454 Chirality : 0.050 0.361 2034 Planarity : 0.006 0.060 2362 Dihedral : 7.128 35.294 1822 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.67 % Favored : 89.20 % Rotamer: Outliers : 0.34 % Allowed : 4.67 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.19), residues: 1630 helix: -1.47 (0.25), residues: 324 sheet: -1.59 (0.27), residues: 362 loop : -2.82 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 544 TYR 0.023 0.003 TYR D 254 PHE 0.020 0.002 PHE F 393 TRP 0.016 0.002 TRP E 139 HIS 0.011 0.002 HIS E 81 Details of bonding type rmsd covalent geometry : bond 0.00544 (13406) covalent geometry : angle 0.88174 (18172) SS BOND : bond 0.00652 ( 51) SS BOND : angle 2.05015 ( 102) hydrogen bonds : bond 0.04915 ( 402) hydrogen bonds : angle 7.03952 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7896 (tttt) cc_final: 0.7483 (mmmt) REVERT: A 181 PRO cc_start: 0.8060 (Cg_endo) cc_final: 0.7736 (Cg_exo) REVERT: E 289 GLU cc_start: 0.8559 (tp30) cc_final: 0.8083 (tp30) REVERT: B 125 LEU cc_start: 0.6282 (mt) cc_final: 0.6002 (mt) REVERT: B 181 PRO cc_start: 0.8612 (Cg_endo) cc_final: 0.8403 (Cg_exo) REVERT: D 297 MET cc_start: 0.6866 (mmm) cc_final: 0.6407 (mmm) REVERT: F 289 GLU cc_start: 0.8534 (tp30) cc_final: 0.8060 (tp30) outliers start: 5 outliers final: 2 residues processed: 179 average time/residue: 0.1182 time to fit residues: 30.6139 Evaluate side-chains 126 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 109 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 106 optimal weight: 0.0980 chunk 154 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN F 81 HIS ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.159467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.140833 restraints weight = 45935.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.143063 restraints weight = 32266.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.144038 restraints weight = 23373.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.144810 restraints weight = 19500.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.145109 restraints weight = 17453.849| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5724 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 13457 Z= 0.171 Angle : 0.784 13.583 18274 Z= 0.398 Chirality : 0.047 0.337 2034 Planarity : 0.005 0.049 2362 Dihedral : 6.540 26.500 1822 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.19), residues: 1630 helix: -1.27 (0.25), residues: 328 sheet: -1.49 (0.27), residues: 378 loop : -2.67 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 226 TYR 0.019 0.002 TYR D 254 PHE 0.016 0.002 PHE D 263 TRP 0.012 0.001 TRP D 312 HIS 0.014 0.001 HIS F 81 Details of bonding type rmsd covalent geometry : bond 0.00410 (13406) covalent geometry : angle 0.76585 (18172) SS BOND : bond 0.00496 ( 51) SS BOND : angle 2.38477 ( 102) hydrogen bonds : bond 0.04107 ( 402) hydrogen bonds : angle 6.53644 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8026 (tttt) cc_final: 0.7417 (mmmt) REVERT: A 181 PRO cc_start: 0.8079 (Cg_endo) cc_final: 0.7722 (Cg_exo) REVERT: C 159 LYS cc_start: 0.7182 (tmmt) cc_final: 0.6727 (tmtt) REVERT: E 289 GLU cc_start: 0.8520 (tp30) cc_final: 0.8030 (tp30) REVERT: E 617 LYS cc_start: 0.7306 (ttmt) cc_final: 0.6683 (mttm) REVERT: D 184 ASN cc_start: 0.7792 (t0) cc_final: 0.7315 (p0) REVERT: D 297 MET cc_start: 0.6849 (mmm) cc_final: 0.6261 (mmm) REVERT: D 323 GLU cc_start: 0.6494 (pp20) cc_final: 0.6106 (pt0) REVERT: F 289 GLU cc_start: 0.8535 (tp30) cc_final: 0.8079 (tp30) REVERT: F 617 LYS cc_start: 0.7268 (ttmt) cc_final: 0.6565 (mttm) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.1205 time to fit residues: 29.3739 Evaluate side-chains 132 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 17 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN E 81 HIS ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.157660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.138951 restraints weight = 47009.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.140492 restraints weight = 34762.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.141662 restraints weight = 25684.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.142023 restraints weight = 23267.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.142249 restraints weight = 20781.669| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 13457 Z= 0.185 Angle : 0.793 16.993 18274 Z= 0.404 Chirality : 0.048 0.330 2034 Planarity : 0.005 0.057 2362 Dihedral : 6.445 33.780 1822 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.14 % Allowed : 3.18 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.19), residues: 1630 helix: -1.09 (0.26), residues: 328 sheet: -1.66 (0.27), residues: 378 loop : -2.64 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 112 TYR 0.021 0.002 TYR B 197 PHE 0.018 0.002 PHE D 263 TRP 0.019 0.002 TRP E 139 HIS 0.013 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00438 (13406) covalent geometry : angle 0.77649 (18172) SS BOND : bond 0.00580 ( 51) SS BOND : angle 2.30665 ( 102) hydrogen bonds : bond 0.04351 ( 402) hydrogen bonds : angle 6.51891 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8159 (tttt) cc_final: 0.7628 (mmmt) REVERT: A 181 PRO cc_start: 0.8132 (Cg_endo) cc_final: 0.7831 (Cg_exo) REVERT: E 289 GLU cc_start: 0.8438 (tp30) cc_final: 0.7913 (tp30) REVERT: E 290 ASP cc_start: 0.7263 (m-30) cc_final: 0.7000 (m-30) REVERT: E 519 CYS cc_start: 0.2359 (m) cc_final: 0.2132 (m) REVERT: E 617 LYS cc_start: 0.7422 (ttmt) cc_final: 0.6931 (mtpt) REVERT: B 125 LEU cc_start: 0.6526 (mt) cc_final: 0.6118 (mt) REVERT: B 155 THR cc_start: 0.7763 (m) cc_final: 0.7503 (m) REVERT: D 184 ASN cc_start: 0.7858 (t0) cc_final: 0.7329 (p0) REVERT: F 289 GLU cc_start: 0.8503 (tp30) cc_final: 0.7978 (tp30) REVERT: F 290 ASP cc_start: 0.7253 (m-30) cc_final: 0.7033 (m-30) REVERT: F 519 CYS cc_start: 0.2294 (m) cc_final: 0.2087 (m) REVERT: F 617 LYS cc_start: 0.7400 (ttmt) cc_final: 0.6823 (mtpt) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.1146 time to fit residues: 27.4824 Evaluate side-chains 120 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 163 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 131 optimal weight: 40.0000 chunk 71 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 79 optimal weight: 0.4980 chunk 91 optimal weight: 20.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS E 187 GLN D 253 ASN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS F 187 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.157335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.139817 restraints weight = 46896.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.140655 restraints weight = 33369.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.141338 restraints weight = 25541.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.141994 restraints weight = 23533.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.142120 restraints weight = 20971.574| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 13457 Z= 0.182 Angle : 0.786 18.409 18274 Z= 0.400 Chirality : 0.048 0.297 2034 Planarity : 0.005 0.051 2362 Dihedral : 6.431 36.372 1822 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.19), residues: 1630 helix: -0.91 (0.26), residues: 322 sheet: -1.72 (0.27), residues: 382 loop : -2.53 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 112 TYR 0.024 0.002 TYR B 197 PHE 0.033 0.002 PHE A 142 TRP 0.013 0.002 TRP F 334 HIS 0.021 0.001 HIS E 81 Details of bonding type rmsd covalent geometry : bond 0.00426 (13406) covalent geometry : angle 0.77106 (18172) SS BOND : bond 0.00616 ( 51) SS BOND : angle 2.15862 ( 102) hydrogen bonds : bond 0.04232 ( 402) hydrogen bonds : angle 6.52940 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8075 (tttt) cc_final: 0.7467 (mmmt) REVERT: A 181 PRO cc_start: 0.8157 (Cg_endo) cc_final: 0.7908 (Cg_exo) REVERT: E 289 GLU cc_start: 0.8568 (tp30) cc_final: 0.8044 (tp30) REVERT: E 290 ASP cc_start: 0.7240 (m-30) cc_final: 0.6983 (m-30) REVERT: E 617 LYS cc_start: 0.7500 (ttmt) cc_final: 0.6817 (mttp) REVERT: D 184 ASN cc_start: 0.7902 (t0) cc_final: 0.7218 (p0) REVERT: F 289 GLU cc_start: 0.8587 (tp30) cc_final: 0.8067 (tp30) REVERT: F 290 ASP cc_start: 0.7227 (m-30) cc_final: 0.7005 (m-30) REVERT: F 617 LYS cc_start: 0.7459 (ttmt) cc_final: 0.6684 (mttp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1213 time to fit residues: 30.2553 Evaluate side-chains 133 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 35 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN C 253 ASN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN E 186 HIS E 187 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS F 187 GLN ** F 333 HIS ** 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 = 0.4627 r_free = 0.4627 target = 0.161768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.143610 restraints weight = 45914.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.145518 restraints weight = 33033.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.147283 restraints weight = 23988.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.147833 restraints weight = 19105.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.147997 restraints weight = 16855.930| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13457 Z= 0.131 Angle : 0.726 18.623 18274 Z= 0.365 Chirality : 0.046 0.262 2034 Planarity : 0.005 0.046 2362 Dihedral : 5.934 33.265 1822 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.20), residues: 1630 helix: -0.56 (0.27), residues: 316 sheet: -1.69 (0.26), residues: 394 loop : -2.28 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 175 TYR 0.029 0.002 TYR D 174 PHE 0.014 0.002 PHE D 263 TRP 0.013 0.001 TRP F 85 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00313 (13406) covalent geometry : angle 0.71459 (18172) SS BOND : bond 0.00474 ( 51) SS BOND : angle 1.86783 ( 102) hydrogen bonds : bond 0.03735 ( 402) hydrogen bonds : angle 6.14405 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PRO cc_start: 0.8176 (Cg_endo) cc_final: 0.7876 (Cg_exo) REVERT: A 189 SER cc_start: 0.7255 (m) cc_final: 0.6914 (m) REVERT: E 289 GLU cc_start: 0.8525 (tp30) cc_final: 0.8161 (tp30) REVERT: E 290 ASP cc_start: 0.7414 (m-30) cc_final: 0.7197 (m-30) REVERT: E 617 LYS cc_start: 0.7392 (ttmt) cc_final: 0.6707 (mttp) REVERT: D 225 ARG cc_start: 0.6068 (ttm170) cc_final: 0.5863 (ttm170) REVERT: D 297 MET cc_start: 0.6870 (mmm) cc_final: 0.6446 (mmm) REVERT: F 289 GLU cc_start: 0.8573 (tp30) cc_final: 0.8202 (tp30) REVERT: F 290 ASP cc_start: 0.7393 (m-30) cc_final: 0.7186 (m-30) REVERT: F 617 LYS cc_start: 0.7391 (ttmt) cc_final: 0.6662 (mttp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1093 time to fit residues: 29.9405 Evaluate side-chains 134 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 ASN E 187 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.164218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.146351 restraints weight = 46556.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.148537 restraints weight = 31527.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.150138 restraints weight = 23327.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.151362 restraints weight = 18198.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.152080 restraints weight = 14876.662| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5519 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 13457 Z= 0.124 Angle : 0.700 18.144 18274 Z= 0.350 Chirality : 0.045 0.242 2034 Planarity : 0.005 0.072 2362 Dihedral : 5.550 31.231 1822 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.20), residues: 1630 helix: -0.36 (0.27), residues: 328 sheet: -1.58 (0.25), residues: 430 loop : -2.15 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 225 TYR 0.029 0.002 TYR D 174 PHE 0.014 0.001 PHE D 263 TRP 0.011 0.001 TRP E 139 HIS 0.004 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00293 (13406) covalent geometry : angle 0.68876 (18172) SS BOND : bond 0.00447 ( 51) SS BOND : angle 1.79016 ( 102) hydrogen bonds : bond 0.03504 ( 402) hydrogen bonds : angle 5.89913 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PRO cc_start: 0.8083 (Cg_endo) cc_final: 0.7801 (Cg_exo) REVERT: C 297 MET cc_start: 0.6373 (mmm) cc_final: 0.5987 (tpp) REVERT: C 322 LEU cc_start: 0.6703 (tt) cc_final: 0.6383 (tt) REVERT: E 95 LEU cc_start: 0.8003 (mp) cc_final: 0.7786 (tp) REVERT: E 287 ARG cc_start: 0.7254 (mtt-85) cc_final: 0.6874 (mmt-90) REVERT: E 289 GLU cc_start: 0.8475 (tp30) cc_final: 0.8171 (tp30) REVERT: E 617 LYS cc_start: 0.7376 (ttmt) cc_final: 0.6798 (mttp) REVERT: D 297 MET cc_start: 0.6873 (tpt) cc_final: 0.6409 (tpt) REVERT: F 287 ARG cc_start: 0.7234 (mtt-85) cc_final: 0.6914 (mmt-90) REVERT: F 289 GLU cc_start: 0.8487 (tp30) cc_final: 0.8186 (tp30) REVERT: F 617 LYS cc_start: 0.7243 (ttmt) cc_final: 0.6604 (mttp) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1187 time to fit residues: 28.7549 Evaluate side-chains 129 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 139 optimal weight: 0.3980 chunk 6 optimal weight: 7.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN E 44 GLN ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN F 44 GLN F 81 HIS ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN F 403 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.156230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.137436 restraints weight = 46668.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.139743 restraints weight = 33292.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.140563 restraints weight = 22984.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.141231 restraints weight = 20516.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.141450 restraints weight = 18451.507| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 13457 Z= 0.217 Angle : 0.842 17.283 18274 Z= 0.427 Chirality : 0.049 0.271 2034 Planarity : 0.006 0.069 2362 Dihedral : 6.218 35.496 1822 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.20), residues: 1630 helix: -0.85 (0.26), residues: 324 sheet: -1.54 (0.26), residues: 390 loop : -2.38 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 225 TYR 0.034 0.003 TYR B 197 PHE 0.023 0.002 PHE D 263 TRP 0.015 0.002 TRP F 334 HIS 0.006 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00498 (13406) covalent geometry : angle 0.82862 (18172) SS BOND : bond 0.00603 ( 51) SS BOND : angle 2.13561 ( 102) hydrogen bonds : bond 0.04668 ( 402) hydrogen bonds : angle 6.45551 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 337 GLU cc_start: 0.6852 (tp30) cc_final: 0.6483 (tp30) REVERT: E 617 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7187 (mttp) REVERT: B 155 THR cc_start: 0.7640 (m) cc_final: 0.7123 (m) REVERT: B 158 LYS cc_start: 0.8937 (mptt) cc_final: 0.8680 (mmtp) REVERT: D 184 ASN cc_start: 0.7913 (t0) cc_final: 0.7202 (p0) REVERT: F 337 GLU cc_start: 0.6666 (tp30) cc_final: 0.6322 (tp30) REVERT: F 617 LYS cc_start: 0.7780 (ttmt) cc_final: 0.7042 (mttp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1057 time to fit residues: 27.8676 Evaluate side-chains 128 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 147 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN E 187 GLN E 421 GLN ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.154982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.136600 restraints weight = 48514.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.138832 restraints weight = 35377.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.139653 restraints weight = 24400.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.139940 restraints weight = 22506.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.140185 restraints weight = 20987.013| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5887 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13457 Z= 0.214 Angle : 0.850 17.299 18274 Z= 0.431 Chirality : 0.049 0.259 2034 Planarity : 0.006 0.070 2362 Dihedral : 6.513 34.720 1822 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.19), residues: 1630 helix: -1.15 (0.25), residues: 324 sheet: -1.57 (0.26), residues: 404 loop : -2.40 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 225 TYR 0.035 0.003 TYR B 197 PHE 0.025 0.002 PHE D 200 TRP 0.015 0.002 TRP F 85 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00496 (13406) covalent geometry : angle 0.83748 (18172) SS BOND : bond 0.00642 ( 51) SS BOND : angle 2.13431 ( 102) hydrogen bonds : bond 0.04745 ( 402) hydrogen bonds : angle 6.65292 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.493 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: E 289 GLU cc_start: 0.7526 (mm-30) cc_final: 0.6060 (tp30) REVERT: E 617 LYS cc_start: 0.7842 (ttmt) cc_final: 0.7077 (tttt) REVERT: D 184 ASN cc_start: 0.7623 (t0) cc_final: 0.7222 (p0) REVERT: F 289 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6070 (tp30) REVERT: F 617 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7128 (tttt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1170 time to fit residues: 28.0047 Evaluate side-chains 131 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 123 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 ASN E 187 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.155267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.136761 restraints weight = 49085.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.138832 restraints weight = 33589.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.140296 restraints weight = 25049.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.141360 restraints weight = 19909.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.141989 restraints weight = 16640.841| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5842 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13457 Z= 0.195 Angle : 0.817 17.268 18274 Z= 0.415 Chirality : 0.048 0.251 2034 Planarity : 0.006 0.068 2362 Dihedral : 6.429 34.116 1822 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.20), residues: 1630 helix: -1.03 (0.26), residues: 322 sheet: -1.55 (0.27), residues: 392 loop : -2.34 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 225 TYR 0.031 0.002 TYR B 197 PHE 0.024 0.002 PHE D 200 TRP 0.016 0.002 TRP F 85 HIS 0.017 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00456 (13406) covalent geometry : angle 0.80516 (18172) SS BOND : bond 0.00585 ( 51) SS BOND : angle 2.04966 ( 102) hydrogen bonds : bond 0.04618 ( 402) hydrogen bonds : angle 6.58622 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1967.76 seconds wall clock time: 34 minutes 55.48 seconds (2095.48 seconds total)