Starting phenix.real_space_refine on Thu Sep 18 05:52:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eio_48088/09_2025/9eio_48088.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eio_48088/09_2025/9eio_48088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eio_48088/09_2025/9eio_48088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eio_48088/09_2025/9eio_48088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eio_48088/09_2025/9eio_48088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eio_48088/09_2025/9eio_48088.map" } resolution = 3.62 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= 1.000 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 S 116 5.16 5 C 9358 2.51 5 N 2515 2.21 5 O 2653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14654 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2652 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2652 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2652 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2652 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1006 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "F" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1005 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "G" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1005 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1014 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.84, per 1000 atoms: 0.26 Number of scatterers: 14654 At special positions: 0 Unit cell: (144.48, 145.34, 100.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 116 16.00 O 2653 8.00 N 2515 7.00 C 9358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 371 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 371 " distance=2.03 Simple disulfide: pdb=" SG CYS D 333 " - pdb=" SG CYS D 371 " distance=2.03 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: 1.31 Conformation dependent library (CDL) restraints added in 697.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 0 sheets defined 71.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 118 through 145 removed outlier: 4.166A pdb=" N ARG A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 158 removed outlier: 3.599A pdb=" N VAL A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 202 removed outlier: 3.943A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.551A pdb=" N CYS A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 268 through 275 removed outlier: 3.807A pdb=" N ARG A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.719A pdb=" N ARG A 287 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 288 " --> pdb=" O SER A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 288' Processing helix chain 'A' and resid 300 through 307 Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.636A pdb=" N PHE A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.849A pdb=" N ARG A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 369 through 382 removed outlier: 4.361A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 380 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.805A pdb=" N VAL A 390 " --> pdb=" O CYS A 386 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 419 through 439 removed outlier: 3.598A pdb=" N ILE A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 476 removed outlier: 4.034A pdb=" N HIS A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN A 462 " --> pdb=" O GLN A 458 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP A 475 " --> pdb=" O ARG A 471 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.633A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 158 removed outlier: 4.100A pdb=" N ILE B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 201 removed outlier: 4.092A pdb=" N LYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.761A pdb=" N ARG B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 291 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.719A pdb=" N PHE B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 327 through 335 removed outlier: 3.896A pdb=" N ARG B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 358 removed outlier: 3.981A pdb=" N LEU B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 4.586A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 404 through 415 removed outlier: 3.700A pdb=" N HIS B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 419 through 439 removed outlier: 4.151A pdb=" N ALA B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 474 removed outlier: 3.659A pdb=" N VAL B 449 " --> pdb=" O ASP B 445 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS B 452 " --> pdb=" O LYS B 448 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N HIS B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN B 462 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN B 474 " --> pdb=" O GLN B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'C' and resid 119 through 134 removed outlier: 3.781A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 145 removed outlier: 3.818A pdb=" N LEU C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 141 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 142 " --> pdb=" O TYR C 138 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 158 removed outlier: 3.592A pdb=" N VAL C 149 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 201 removed outlier: 4.045A pdb=" N LYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 183 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.564A pdb=" N PHE C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS C 219 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU C 221 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 268 through 275 removed outlier: 3.687A pdb=" N ARG C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.966A pdb=" N ASN C 293 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.721A pdb=" N THR C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 321 removed outlier: 3.643A pdb=" N PHE C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 327 through 334 removed outlier: 3.850A pdb=" N ARG C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 Processing helix chain 'C' and resid 371 through 382 removed outlier: 4.280A pdb=" N LEU C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 397 Processing helix chain 'C' and resid 402 through 415 removed outlier: 4.387A pdb=" N VAL C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N HIS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 419 through 439 removed outlier: 3.729A pdb=" N ALA C 423 " --> pdb=" O ARG C 419 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 448 Processing helix chain 'C' and resid 449 through 457 removed outlier: 3.855A pdb=" N LYS C 455 " --> pdb=" O LYS C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 476 removed outlier: 4.157A pdb=" N HIS C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN C 462 " --> pdb=" O GLN C 458 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU C 463 " --> pdb=" O ALA C 459 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU C 469 " --> pdb=" O SER C 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 134 removed outlier: 4.214A pdb=" N ARG D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 158 removed outlier: 3.917A pdb=" N LEU D 140 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 141 " --> pdb=" O ASP D 137 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE D 142 " --> pdb=" O TYR D 138 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY D 146 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 147 " --> pdb=" O GLY D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 201 removed outlier: 4.043A pdb=" N LYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU D 183 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN D 201 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 226 removed outlier: 3.619A pdb=" N ILE D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 260 through 264 removed outlier: 3.556A pdb=" N PHE D 264 " --> pdb=" O ILE D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 268 through 275 removed outlier: 3.693A pdb=" N ARG D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 300 through 310 removed outlier: 3.615A pdb=" N THR D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS D 310 " --> pdb=" O LEU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 317 Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.681A pdb=" N ARG D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 351 through 358 Processing helix chain 'D' and resid 371 through 382 removed outlier: 6.379A pdb=" N LEU D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 398 removed outlier: 3.957A pdb=" N VAL D 390 " --> pdb=" O CYS D 386 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 391 " --> pdb=" O THR D 387 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA D 392 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 415 removed outlier: 4.649A pdb=" N VAL D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 419 through 439 removed outlier: 3.791A pdb=" N TYR D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 477 removed outlier: 3.771A pdb=" N VAL D 449 " --> pdb=" O ASP D 445 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS D 452 " --> pdb=" O LYS D 448 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN D 462 " --> pdb=" O GLN D 458 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU D 463 " --> pdb=" O ALA D 459 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 469 " --> pdb=" O SER D 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 8 Processing helix chain 'E' and resid 9 through 20 removed outlier: 3.742A pdb=" N PHE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 removed outlier: 3.534A pdb=" N LEU E 32 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.882A pdb=" N VAL E 55 " --> pdb=" O MET E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 73 removed outlier: 4.031A pdb=" N THR E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 88 removed outlier: 4.256A pdb=" N ARG E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 101 through 111 Processing helix chain 'E' and resid 117 through 128 removed outlier: 5.975A pdb=" N MET E 124 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.857A pdb=" N GLU E 140 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE E 141 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN E 143 " --> pdb=" O GLU E 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 8 Processing helix chain 'F' and resid 9 through 19 removed outlier: 4.412A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 removed outlier: 3.769A pdb=" N SER F 38 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU F 39 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY F 40 " --> pdb=" O MET F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 54 removed outlier: 4.131A pdb=" N GLU F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 73 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 101 through 111 Processing helix chain 'F' and resid 117 through 122 Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 137 through 144 removed outlier: 4.316A pdb=" N GLU F 140 " --> pdb=" O ASN F 137 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE F 141 " --> pdb=" O TYR F 138 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN F 143 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 20 Processing helix chain 'G' and resid 28 through 40 removed outlier: 3.541A pdb=" N THR G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU G 39 " --> pdb=" O VAL G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 53 Processing helix chain 'G' and resid 64 through 73 removed outlier: 3.801A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET G 71 " --> pdb=" O GLU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 92 Processing helix chain 'G' and resid 104 through 112 Processing helix chain 'G' and resid 119 through 128 removed outlier: 4.083A pdb=" N GLU G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU G 127 " --> pdb=" O GLU G 123 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA G 128 " --> pdb=" O MET G 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 19 removed outlier: 3.682A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 36 Processing helix chain 'H' and resid 44 through 53 Processing helix chain 'H' and resid 64 through 73 removed outlier: 3.567A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 93 removed outlier: 4.240A pdb=" N GLU H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE H 85 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG H 86 " --> pdb=" O GLU H 82 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE H 89 " --> pdb=" O ILE H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 112 removed outlier: 3.505A pdb=" N LEU H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 127 removed outlier: 4.050A pdb=" N GLU H 123 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 132 removed outlier: 3.601A pdb=" N ASP H 131 " --> pdb=" O ALA H 128 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 2052 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: 2.18 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4795 1.34 - 1.46: 2982 1.46 - 1.58: 6893 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 14870 Sorted by residual: bond pdb=" CA GLY G 134 " pdb=" C GLY G 134 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.60e+00 bond pdb=" N GLY G 134 " pdb=" CA GLY G 134 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.91e+00 bond pdb=" CB GLU C 430 " pdb=" CG GLU C 430 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" N GLN B 340 " pdb=" CA GLN B 340 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.05e+00 bond pdb=" CA LYS A 397 " pdb=" C LYS A 397 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.80e-02 3.09e+03 8.06e-01 ... (remaining 14865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 19271 1.14 - 2.28: 636 2.28 - 3.42: 123 3.42 - 4.56: 46 4.56 - 5.70: 16 Bond angle restraints: 20092 Sorted by residual: angle pdb=" N ILE A 257 " pdb=" CA ILE A 257 " pdb=" C ILE A 257 " ideal model delta sigma weight residual 112.96 108.16 4.80 1.00e+00 1.00e+00 2.30e+01 angle pdb=" N ILE D 257 " pdb=" CA ILE D 257 " pdb=" C ILE D 257 " ideal model delta sigma weight residual 113.42 107.91 5.51 1.17e+00 7.31e-01 2.22e+01 angle pdb=" N ILE C 257 " pdb=" CA ILE C 257 " pdb=" C ILE C 257 " ideal model delta sigma weight residual 112.96 108.37 4.59 1.00e+00 1.00e+00 2.10e+01 angle pdb=" N THR C 343 " pdb=" CA THR C 343 " pdb=" C THR C 343 " ideal model delta sigma weight residual 112.94 107.90 5.04 1.41e+00 5.03e-01 1.28e+01 angle pdb=" C LEU B 122 " pdb=" CA LEU B 122 " pdb=" CB LEU B 122 " ideal model delta sigma weight residual 115.79 112.03 3.76 1.19e+00 7.06e-01 1.00e+01 ... (remaining 20087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8088 17.98 - 35.97: 705 35.97 - 53.95: 121 53.95 - 71.93: 19 71.93 - 89.92: 15 Dihedral angle restraints: 8948 sinusoidal: 3368 harmonic: 5580 Sorted by residual: dihedral pdb=" CB CYS A 333 " pdb=" SG CYS A 333 " pdb=" SG CYS A 371 " pdb=" CB CYS A 371 " ideal model delta sinusoidal sigma weight residual 93.00 27.64 65.36 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CB CYS C 333 " pdb=" SG CYS C 333 " pdb=" SG CYS C 371 " pdb=" CB CYS C 371 " ideal model delta sinusoidal sigma weight residual 93.00 29.97 63.03 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS B 333 " pdb=" SG CYS B 333 " pdb=" SG CYS B 371 " pdb=" CB CYS B 371 " ideal model delta sinusoidal sigma weight residual 93.00 32.88 60.12 1 1.00e+01 1.00e-02 4.82e+01 ... (remaining 8945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1331 0.030 - 0.060: 772 0.060 - 0.090: 210 0.090 - 0.120: 45 0.120 - 0.150: 11 Chirality restraints: 2369 Sorted by residual: chirality pdb=" CA VAL A 366 " pdb=" N VAL A 366 " pdb=" C VAL A 366 " pdb=" CB VAL A 366 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA VAL D 366 " pdb=" N VAL D 366 " pdb=" C VAL D 366 " pdb=" CB VAL D 366 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CG LEU C 174 " pdb=" CB LEU C 174 " pdb=" CD1 LEU C 174 " pdb=" CD2 LEU C 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 2366 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 374 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C GLY D 374 " -0.025 2.00e-02 2.50e+03 pdb=" O GLY D 374 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL D 375 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 366 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO D 367 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 228 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO D 229 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO D 229 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 229 " -0.014 5.00e-02 4.00e+02 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 3769 2.79 - 3.38: 16026 3.38 - 3.97: 24135 3.97 - 4.55: 34087 4.55 - 5.14: 49952 Nonbonded interactions: 127969 Sorted by model distance: nonbonded pdb=" OE1 GLU B 334 " pdb=" OG1 THR B 343 " model vdw 2.208 3.040 nonbonded pdb=" O MET C 412 " pdb=" OG1 THR C 417 " model vdw 2.224 3.040 nonbonded pdb=" O SER B 278 " pdb=" OG1 THR B 282 " model vdw 2.240 3.040 nonbonded pdb=" O PHE B 281 " pdb=" NH2 ARG B 287 " model vdw 2.300 3.120 nonbonded pdb=" NE2 GLN C 470 " pdb=" OD1 ASN C 474 " model vdw 2.302 3.120 ... (remaining 127964 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 118 through 478) selection = chain 'B' selection = (chain 'C' and resid 118 through 478) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 3 through 100 or (resid 101 through 108 and (name N or nam \ e CA or name C or name O or name CB )) or resid 109 through 202)) selection = chain 'F' selection = chain 'G' selection = (chain 'H' and (resid 3 through 99 or (resid 100 through 108 and (name N or name \ CA or name C or name O or name CB )) or resid 109 through 202)) } 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: 12.950 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: 0.030 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.680 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 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 : 0.002 0.045 14874 Z= 0.117 Angle : 0.535 5.700 20100 Z= 0.296 Chirality : 0.039 0.150 2369 Planarity : 0.002 0.026 2529 Dihedral : 14.219 89.917 5312 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.19), residues: 1900 helix: -0.95 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -2.10 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 429 TYR 0.012 0.001 TYR D 362 PHE 0.010 0.001 PHE D 456 TRP 0.017 0.001 TRP C 351 HIS 0.006 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00250 (14870) covalent geometry : angle 0.53515 (20092) SS BOND : bond 0.00428 ( 4) SS BOND : angle 0.20057 ( 8) hydrogen bonds : bond 0.10688 ( 703) hydrogen bonds : angle 4.51008 ( 2052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 ASP cc_start: 0.5562 (m-30) cc_final: 0.5305 (m-30) REVERT: C 413 ASP cc_start: 0.7785 (t0) cc_final: 0.7563 (t0) REVERT: E 24 ASP cc_start: 0.6718 (p0) cc_final: 0.5232 (t0) REVERT: F 83 GLU cc_start: 0.6409 (pm20) cc_final: 0.6023 (pm20) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1223 time to fit residues: 62.8553 Evaluate side-chains 306 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0030 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.5048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 ASN D 470 GLN E 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.276654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.263243 restraints weight = 16241.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.259173 restraints weight = 25140.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.257383 restraints weight = 30438.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.256886 restraints weight = 27250.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.255654 restraints weight = 21193.896| |-----------------------------------------------------------------------------| r_work (final): 0.4785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14874 Z= 0.118 Angle : 0.561 7.361 20100 Z= 0.296 Chirality : 0.038 0.148 2369 Planarity : 0.003 0.041 2529 Dihedral : 4.393 26.263 2049 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.11 % Allowed : 10.74 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.20), residues: 1900 helix: -0.84 (0.15), residues: 1287 sheet: None (None), residues: 0 loop : -2.02 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 287 TYR 0.018 0.001 TYR A 435 PHE 0.016 0.001 PHE H 16 TRP 0.015 0.001 TRP A 351 HIS 0.003 0.001 HIS B 461 Details of bonding type rmsd covalent geometry : bond 0.00267 (14870) covalent geometry : angle 0.56098 (20092) SS BOND : bond 0.00359 ( 4) SS BOND : angle 0.25343 ( 8) hydrogen bonds : bond 0.03340 ( 703) hydrogen bonds : angle 3.89673 ( 2052) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 305 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 162 ASP cc_start: 0.5284 (m-30) cc_final: 0.5058 (m-30) REVERT: D 294 LYS cc_start: 0.6478 (mmtt) cc_final: 0.6246 (mmtt) REVERT: D 316 LEU cc_start: 0.8501 (tt) cc_final: 0.8282 (tp) REVERT: E 22 ASP cc_start: 0.6113 (p0) cc_final: 0.5693 (p0) REVERT: E 24 ASP cc_start: 0.6654 (p0) cc_final: 0.5225 (t0) REVERT: E 26 THR cc_start: 0.7846 (p) cc_final: 0.7634 (p) REVERT: E 36 MET cc_start: 0.7608 (mtp) cc_final: 0.7258 (mtp) REVERT: F 83 GLU cc_start: 0.6488 (pm20) cc_final: 0.6101 (pm20) REVERT: H 20 ASP cc_start: 0.4449 (t0) cc_final: 0.4229 (t0) REVERT: H 22 ASP cc_start: 0.5809 (p0) cc_final: 0.5155 (p0) REVERT: H 24 ASP cc_start: 0.6444 (p0) cc_final: 0.3444 (t0) outliers start: 31 outliers final: 17 residues processed: 314 average time/residue: 0.1168 time to fit residues: 54.5916 Evaluate side-chains 308 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 291 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 158 optimal weight: 0.0010 chunk 143 optimal weight: 20.0000 chunk 37 optimal weight: 0.1980 chunk 104 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 470 GLN B 437 ASN B 470 GLN ** G 41 GLN ** 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 = 0.4969 r_free = 0.4969 target = 0.277934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.263493 restraints weight = 16784.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.259719 restraints weight = 23371.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.256178 restraints weight = 21501.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.254696 restraints weight = 19802.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.253446 restraints weight = 18266.237| |-----------------------------------------------------------------------------| r_work (final): 0.4770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14874 Z= 0.105 Angle : 0.526 7.508 20100 Z= 0.279 Chirality : 0.037 0.147 2369 Planarity : 0.003 0.025 2529 Dihedral : 4.232 26.044 2049 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.45 % Allowed : 13.60 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.20), residues: 1900 helix: -0.70 (0.15), residues: 1287 sheet: None (None), residues: 0 loop : -1.94 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 37 TYR 0.015 0.001 TYR H 138 PHE 0.018 0.001 PHE F 68 TRP 0.014 0.001 TRP A 351 HIS 0.002 0.000 HIS D 461 Details of bonding type rmsd covalent geometry : bond 0.00230 (14870) covalent geometry : angle 0.52650 (20092) SS BOND : bond 0.00287 ( 4) SS BOND : angle 0.19608 ( 8) hydrogen bonds : bond 0.02937 ( 703) hydrogen bonds : angle 3.74657 ( 2052) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 295 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8244 (ptp) REVERT: D 294 LYS cc_start: 0.6577 (mmtt) cc_final: 0.6374 (mmtt) REVERT: D 316 LEU cc_start: 0.8496 (tt) cc_final: 0.8295 (tp) REVERT: E 24 ASP cc_start: 0.6816 (p0) cc_final: 0.5528 (t0) REVERT: E 36 MET cc_start: 0.7731 (mtp) cc_final: 0.7476 (mtp) REVERT: F 71 MET cc_start: 0.8120 (tmm) cc_final: 0.7275 (tmm) REVERT: F 83 GLU cc_start: 0.6601 (pm20) cc_final: 0.6034 (pm20) REVERT: H 22 ASP cc_start: 0.5875 (p0) cc_final: 0.5277 (p0) REVERT: H 24 ASP cc_start: 0.6577 (p0) cc_final: 0.3549 (t0) outliers start: 36 outliers final: 23 residues processed: 308 average time/residue: 0.1152 time to fit residues: 52.2376 Evaluate side-chains 308 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 284 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 104 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 173 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 56 optimal weight: 0.0060 chunk 138 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN B 437 ASN B 470 GLN ** G 41 GLN ** 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 = 0.4944 r_free = 0.4944 target = 0.274383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.261413 restraints weight = 16295.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.258734 restraints weight = 22810.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.255458 restraints weight = 17446.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.253724 restraints weight = 18783.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.252710 restraints weight = 18746.544| |-----------------------------------------------------------------------------| r_work (final): 0.4770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14874 Z= 0.141 Angle : 0.557 7.028 20100 Z= 0.293 Chirality : 0.039 0.142 2369 Planarity : 0.003 0.028 2529 Dihedral : 4.367 25.501 2049 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.47 % Allowed : 15.23 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.20), residues: 1900 helix: -0.67 (0.15), residues: 1259 sheet: None (None), residues: 0 loop : -1.95 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 287 TYR 0.018 0.001 TYR A 435 PHE 0.014 0.001 PHE B 456 TRP 0.016 0.002 TRP A 351 HIS 0.003 0.001 HIS D 461 Details of bonding type rmsd covalent geometry : bond 0.00336 (14870) covalent geometry : angle 0.55709 (20092) SS BOND : bond 0.00578 ( 4) SS BOND : angle 0.35913 ( 8) hydrogen bonds : bond 0.03352 ( 703) hydrogen bonds : angle 3.85342 ( 2052) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LEU cc_start: 0.8757 (mt) cc_final: 0.8504 (tt) REVERT: E 22 ASP cc_start: 0.5688 (p0) cc_final: 0.5244 (p0) REVERT: E 24 ASP cc_start: 0.6754 (p0) cc_final: 0.5437 (t0) REVERT: E 36 MET cc_start: 0.7603 (mtp) cc_final: 0.7300 (mtp) REVERT: E 112 LEU cc_start: 0.5475 (OUTLIER) cc_final: 0.4857 (tp) REVERT: F 71 MET cc_start: 0.8123 (tmm) cc_final: 0.7134 (tmm) REVERT: F 83 GLU cc_start: 0.6536 (pm20) cc_final: 0.6060 (pm20) REVERT: H 24 ASP cc_start: 0.6440 (p0) cc_final: 0.5898 (p0) outliers start: 51 outliers final: 32 residues processed: 317 average time/residue: 0.1169 time to fit residues: 54.8995 Evaluate side-chains 322 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 157 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 53 optimal weight: 0.0070 chunk 63 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 78 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.273974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.257511 restraints weight = 16653.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.252095 restraints weight = 23121.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.249204 restraints weight = 21821.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.248498 restraints weight = 20097.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.247041 restraints weight = 15807.207| |-----------------------------------------------------------------------------| r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14874 Z= 0.140 Angle : 0.559 6.760 20100 Z= 0.296 Chirality : 0.039 0.151 2369 Planarity : 0.003 0.031 2529 Dihedral : 4.404 26.509 2049 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.81 % Allowed : 16.52 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.20), residues: 1900 helix: -0.67 (0.15), residues: 1260 sheet: None (None), residues: 0 loop : -1.95 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 287 TYR 0.013 0.001 TYR B 362 PHE 0.013 0.001 PHE B 456 TRP 0.017 0.002 TRP A 351 HIS 0.003 0.001 HIS D 461 Details of bonding type rmsd covalent geometry : bond 0.00332 (14870) covalent geometry : angle 0.55954 (20092) SS BOND : bond 0.00546 ( 4) SS BOND : angle 0.32393 ( 8) hydrogen bonds : bond 0.03328 ( 703) hydrogen bonds : angle 3.85996 ( 2052) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 293 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7554 (mt) REVERT: A 316 LEU cc_start: 0.8799 (mt) cc_final: 0.8541 (tt) REVERT: A 470 GLN cc_start: 0.7795 (tp40) cc_final: 0.7503 (tp40) REVERT: B 470 GLN cc_start: 0.7537 (tp40) cc_final: 0.7254 (tp40) REVERT: E 22 ASP cc_start: 0.5816 (p0) cc_final: 0.5448 (p0) REVERT: E 24 ASP cc_start: 0.7127 (p0) cc_final: 0.5670 (t0) REVERT: E 36 MET cc_start: 0.7689 (mtp) cc_final: 0.7387 (mtp) REVERT: E 112 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.4813 (tp) REVERT: F 71 MET cc_start: 0.8361 (tmm) cc_final: 0.7321 (tmm) REVERT: F 83 GLU cc_start: 0.6531 (pm20) cc_final: 0.6029 (pm20) REVERT: G 72 MET cc_start: 0.8139 (tpt) cc_final: 0.7714 (mmt) REVERT: H 22 ASP cc_start: 0.6062 (p0) cc_final: 0.5383 (p0) REVERT: H 24 ASP cc_start: 0.6513 (p0) cc_final: 0.3449 (t0) outliers start: 56 outliers final: 32 residues processed: 324 average time/residue: 0.1117 time to fit residues: 53.9060 Evaluate side-chains 322 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 288 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 9 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 48 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 155 optimal weight: 0.0270 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN D 470 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.275985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.260568 restraints weight = 16569.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.256266 restraints weight = 23224.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.252890 restraints weight = 21092.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.251437 restraints weight = 18912.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.249062 restraints weight = 19185.150| |-----------------------------------------------------------------------------| r_work (final): 0.4736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14874 Z= 0.112 Angle : 0.532 7.496 20100 Z= 0.282 Chirality : 0.038 0.151 2369 Planarity : 0.003 0.030 2529 Dihedral : 4.261 26.125 2049 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.72 % Allowed : 18.35 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.20), residues: 1900 helix: -0.54 (0.15), residues: 1260 sheet: None (None), residues: 0 loop : -1.91 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 287 TYR 0.009 0.001 TYR B 362 PHE 0.013 0.001 PHE B 456 TRP 0.017 0.001 TRP A 351 HIS 0.002 0.000 HIS A 461 Details of bonding type rmsd covalent geometry : bond 0.00255 (14870) covalent geometry : angle 0.53186 (20092) SS BOND : bond 0.00358 ( 4) SS BOND : angle 0.23699 ( 8) hydrogen bonds : bond 0.02897 ( 703) hydrogen bonds : angle 3.72757 ( 2052) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 292 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7505 (mt) REVERT: A 316 LEU cc_start: 0.8791 (mt) cc_final: 0.8501 (tt) REVERT: A 470 GLN cc_start: 0.7724 (tp40) cc_final: 0.7510 (tp40) REVERT: B 470 GLN cc_start: 0.7603 (tp40) cc_final: 0.7258 (tp40) REVERT: E 22 ASP cc_start: 0.5536 (p0) cc_final: 0.5236 (p0) REVERT: E 24 ASP cc_start: 0.6973 (p0) cc_final: 0.5615 (t0) REVERT: E 36 MET cc_start: 0.7541 (mtp) cc_final: 0.7295 (mtp) REVERT: E 37 ARG cc_start: 0.7267 (mtp85) cc_final: 0.6993 (mmm160) REVERT: E 83 GLU cc_start: 0.6908 (pm20) cc_final: 0.6183 (tp30) REVERT: E 112 LEU cc_start: 0.5475 (OUTLIER) cc_final: 0.4982 (tp) REVERT: F 83 GLU cc_start: 0.6502 (pm20) cc_final: 0.6064 (pm20) REVERT: G 72 MET cc_start: 0.8115 (tpt) cc_final: 0.7371 (mmt) REVERT: H 24 ASP cc_start: 0.6450 (p0) cc_final: 0.3526 (t70) outliers start: 40 outliers final: 26 residues processed: 308 average time/residue: 0.1122 time to fit residues: 51.7183 Evaluate side-chains 315 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 56 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 91 optimal weight: 0.0170 chunk 72 optimal weight: 0.5980 chunk 162 optimal weight: 4.9990 chunk 174 optimal weight: 0.0060 chunk 42 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 84 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.277777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.262266 restraints weight = 16538.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.258374 restraints weight = 23021.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.254532 restraints weight = 24095.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.253501 restraints weight = 21937.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.251740 restraints weight = 19079.498| |-----------------------------------------------------------------------------| r_work (final): 0.4757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14874 Z= 0.100 Angle : 0.527 9.784 20100 Z= 0.278 Chirality : 0.037 0.156 2369 Planarity : 0.002 0.030 2529 Dihedral : 4.127 25.253 2049 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.58 % Allowed : 19.58 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.20), residues: 1900 helix: -0.44 (0.15), residues: 1264 sheet: None (None), residues: 0 loop : -1.83 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 287 TYR 0.007 0.001 TYR B 268 PHE 0.027 0.001 PHE H 68 TRP 0.015 0.001 TRP A 351 HIS 0.002 0.000 HIS B 461 Details of bonding type rmsd covalent geometry : bond 0.00222 (14870) covalent geometry : angle 0.52742 (20092) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.18982 ( 8) hydrogen bonds : bond 0.02650 ( 703) hydrogen bonds : angle 3.63082 ( 2052) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7483 (mt) REVERT: A 287 ARG cc_start: 0.8057 (mmt90) cc_final: 0.7727 (mmt90) REVERT: A 316 LEU cc_start: 0.8681 (mt) cc_final: 0.8434 (tt) REVERT: A 470 GLN cc_start: 0.7763 (tp40) cc_final: 0.7554 (tp40) REVERT: B 470 GLN cc_start: 0.7680 (tp40) cc_final: 0.7395 (tp40) REVERT: E 22 ASP cc_start: 0.5437 (p0) cc_final: 0.5174 (p0) REVERT: E 24 ASP cc_start: 0.6908 (p0) cc_final: 0.5561 (t0) REVERT: E 36 MET cc_start: 0.7445 (mtp) cc_final: 0.7239 (mtp) REVERT: E 37 ARG cc_start: 0.7224 (mtp85) cc_final: 0.6995 (mmm160) REVERT: E 83 GLU cc_start: 0.6915 (pm20) cc_final: 0.6222 (tp30) REVERT: E 112 LEU cc_start: 0.5507 (OUTLIER) cc_final: 0.5096 (mt) REVERT: F 83 GLU cc_start: 0.6697 (pm20) cc_final: 0.6236 (pm20) REVERT: G 72 MET cc_start: 0.8053 (tpt) cc_final: 0.7676 (tpt) REVERT: H 22 ASP cc_start: 0.5941 (p0) cc_final: 0.5392 (p0) REVERT: H 24 ASP cc_start: 0.6374 (p0) cc_final: 0.3773 (t70) outliers start: 38 outliers final: 28 residues processed: 310 average time/residue: 0.1067 time to fit residues: 49.4577 Evaluate side-chains 316 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 286 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.0050 chunk 65 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 77 optimal weight: 0.0980 chunk 181 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.277395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.262109 restraints weight = 16656.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.258194 restraints weight = 22875.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.254511 restraints weight = 20078.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.252106 restraints weight = 19375.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.251001 restraints weight = 20138.728| |-----------------------------------------------------------------------------| r_work (final): 0.4747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14874 Z= 0.108 Angle : 0.533 8.829 20100 Z= 0.282 Chirality : 0.037 0.155 2369 Planarity : 0.003 0.031 2529 Dihedral : 4.094 25.230 2049 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.38 % Allowed : 19.85 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.20), residues: 1900 helix: -0.53 (0.15), residues: 1292 sheet: None (None), residues: 0 loop : -1.75 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 287 TYR 0.007 0.001 TYR B 362 PHE 0.012 0.001 PHE B 456 TRP 0.015 0.001 TRP A 351 HIS 0.010 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00247 (14870) covalent geometry : angle 0.53281 (20092) SS BOND : bond 0.00315 ( 4) SS BOND : angle 0.21119 ( 8) hydrogen bonds : bond 0.02732 ( 703) hydrogen bonds : angle 3.62062 ( 2052) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7488 (mt) REVERT: A 316 LEU cc_start: 0.8659 (mt) cc_final: 0.8451 (tt) REVERT: A 323 TRP cc_start: 0.7289 (m-10) cc_final: 0.6816 (t60) REVERT: E 22 ASP cc_start: 0.5251 (p0) cc_final: 0.4950 (p0) REVERT: E 24 ASP cc_start: 0.6876 (p0) cc_final: 0.5467 (t0) REVERT: E 37 ARG cc_start: 0.7235 (mtp85) cc_final: 0.7020 (mmm160) REVERT: E 83 GLU cc_start: 0.6891 (pm20) cc_final: 0.6261 (tp30) REVERT: E 112 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.5078 (mt) REVERT: F 83 GLU cc_start: 0.6770 (pm20) cc_final: 0.6285 (pm20) REVERT: H 22 ASP cc_start: 0.5968 (p0) cc_final: 0.5404 (p0) REVERT: H 24 ASP cc_start: 0.6393 (p0) cc_final: 0.3785 (t70) outliers start: 35 outliers final: 31 residues processed: 315 average time/residue: 0.1113 time to fit residues: 52.2116 Evaluate side-chains 319 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 114 optimal weight: 4.9990 chunk 55 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 chunk 57 optimal weight: 0.0060 chunk 150 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 111 optimal weight: 0.2980 chunk 88 optimal weight: 0.5980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.278937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.263812 restraints weight = 16638.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.260165 restraints weight = 23219.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.256134 restraints weight = 24736.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.255677 restraints weight = 22606.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.253795 restraints weight = 18225.537| |-----------------------------------------------------------------------------| r_work (final): 0.4775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14874 Z= 0.102 Angle : 0.539 11.448 20100 Z= 0.284 Chirality : 0.037 0.159 2369 Planarity : 0.002 0.031 2529 Dihedral : 4.006 24.664 2049 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.68 % Favored : 92.26 % Rotamer: Outliers : 2.04 % Allowed : 20.26 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.20), residues: 1900 helix: -0.38 (0.15), residues: 1268 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 287 TYR 0.007 0.001 TYR E 138 PHE 0.029 0.001 PHE H 68 TRP 0.014 0.001 TRP A 351 HIS 0.006 0.000 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00230 (14870) covalent geometry : angle 0.53957 (20092) SS BOND : bond 0.00231 ( 4) SS BOND : angle 0.20831 ( 8) hydrogen bonds : bond 0.02541 ( 703) hydrogen bonds : angle 3.55225 ( 2052) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 285 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7459 (mt) REVERT: A 316 LEU cc_start: 0.8666 (mt) cc_final: 0.8400 (tt) REVERT: A 323 TRP cc_start: 0.7214 (m-10) cc_final: 0.6753 (t60) REVERT: B 210 MET cc_start: 0.8069 (mmm) cc_final: 0.7823 (mmm) REVERT: E 24 ASP cc_start: 0.6434 (p0) cc_final: 0.5132 (t0) REVERT: E 83 GLU cc_start: 0.6890 (pm20) cc_final: 0.6266 (tp30) REVERT: E 112 LEU cc_start: 0.5483 (OUTLIER) cc_final: 0.5077 (mt) REVERT: F 83 GLU cc_start: 0.6725 (pm20) cc_final: 0.6030 (tp30) REVERT: H 22 ASP cc_start: 0.5858 (p0) cc_final: 0.5277 (p0) REVERT: H 24 ASP cc_start: 0.6328 (p0) cc_final: 0.3760 (t70) outliers start: 30 outliers final: 27 residues processed: 299 average time/residue: 0.1124 time to fit residues: 49.6416 Evaluate side-chains 306 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 20 optimal weight: 0.0670 chunk 37 optimal weight: 0.0030 chunk 7 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 121 optimal weight: 0.0870 chunk 82 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 overall best weight: 0.2706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN C 201 ASN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.279602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.263746 restraints weight = 16500.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.259479 restraints weight = 23097.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.256320 restraints weight = 19527.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.254812 restraints weight = 18996.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.253050 restraints weight = 18158.082| |-----------------------------------------------------------------------------| r_work (final): 0.4771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 14874 Z= 0.102 Angle : 0.545 10.664 20100 Z= 0.286 Chirality : 0.037 0.180 2369 Planarity : 0.002 0.030 2529 Dihedral : 3.897 24.486 2049 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.68 % Favored : 92.26 % Rotamer: Outliers : 2.38 % Allowed : 19.85 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.20), residues: 1900 helix: -0.34 (0.15), residues: 1290 sheet: None (None), residues: 0 loop : -1.69 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 132 TYR 0.008 0.001 TYR E 138 PHE 0.012 0.001 PHE B 456 TRP 0.013 0.001 TRP A 351 HIS 0.006 0.000 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00229 (14870) covalent geometry : angle 0.54516 (20092) SS BOND : bond 0.00203 ( 4) SS BOND : angle 0.21003 ( 8) hydrogen bonds : bond 0.02463 ( 703) hydrogen bonds : angle 3.48928 ( 2052) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7485 (mt) REVERT: A 316 LEU cc_start: 0.8586 (mt) cc_final: 0.8311 (tt) REVERT: A 323 TRP cc_start: 0.7187 (m-10) cc_final: 0.6861 (t60) REVERT: B 210 MET cc_start: 0.8068 (mmm) cc_final: 0.7847 (mmm) REVERT: C 198 MET cc_start: 0.6718 (mmp) cc_final: 0.6510 (mmp) REVERT: E 22 ASP cc_start: 0.5571 (p0) cc_final: 0.4972 (p0) REVERT: E 24 ASP cc_start: 0.6550 (p0) cc_final: 0.5006 (t0) REVERT: E 83 GLU cc_start: 0.6890 (pm20) cc_final: 0.6293 (tp30) REVERT: E 112 LEU cc_start: 0.5443 (OUTLIER) cc_final: 0.5038 (mt) REVERT: F 83 GLU cc_start: 0.6767 (pm20) cc_final: 0.5999 (tp30) REVERT: G 82 GLU cc_start: 0.6310 (mp0) cc_final: 0.6043 (mm-30) REVERT: H 24 ASP cc_start: 0.6313 (p0) cc_final: 0.3722 (t70) outliers start: 35 outliers final: 31 residues processed: 294 average time/residue: 0.1154 time to fit residues: 50.0958 Evaluate side-chains 303 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 270 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 169 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 167 optimal weight: 6.9990 chunk 139 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.277549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.263234 restraints weight = 16515.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.259556 restraints weight = 23331.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.255335 restraints weight = 21992.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.254121 restraints weight = 21200.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.252452 restraints weight = 19798.973| |-----------------------------------------------------------------------------| r_work (final): 0.4764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14874 Z= 0.122 Angle : 0.570 11.123 20100 Z= 0.298 Chirality : 0.038 0.161 2369 Planarity : 0.003 0.032 2529 Dihedral : 4.035 25.382 2049 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.68 % Favored : 92.26 % Rotamer: Outliers : 2.24 % Allowed : 20.05 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.20), residues: 1900 helix: -0.40 (0.15), residues: 1291 sheet: None (None), residues: 0 loop : -1.72 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 287 TYR 0.008 0.001 TYR A 120 PHE 0.030 0.001 PHE H 68 TRP 0.013 0.001 TRP A 351 HIS 0.006 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00284 (14870) covalent geometry : angle 0.56981 (20092) SS BOND : bond 0.00417 ( 4) SS BOND : angle 0.25631 ( 8) hydrogen bonds : bond 0.02829 ( 703) hydrogen bonds : angle 3.56670 ( 2052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2352.74 seconds wall clock time: 41 minutes 33.60 seconds (2493.60 seconds total)