Starting phenix.real_space_refine on Sun Jul 27 07:53:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jbj_9791/07_2025/6jbj_9791_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jbj_9791/07_2025/6jbj_9791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jbj_9791/07_2025/6jbj_9791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jbj_9791/07_2025/6jbj_9791.map" model { file = "/net/cci-nas-00/data/ceres_data/6jbj_9791/07_2025/6jbj_9791_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jbj_9791/07_2025/6jbj_9791_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 40 5.16 5 C 5914 2.51 5 N 1534 2.21 5 O 1672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9166 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4552 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 19, 'TRANS': 545} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 8.28, per 1000 atoms: 0.90 Number of scatterers: 9166 At special positions: 0 Unit cell: (75.92, 73.84, 130, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 6 15.00 O 1672 8.00 N 1534 7.00 C 5914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 63.9% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 18 through 32 removed outlier: 4.193A pdb=" N GLN A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 61 removed outlier: 3.936A pdb=" N THR A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 46 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 52 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 75 through 124 removed outlier: 3.877A pdb=" N THR A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 135 removed outlier: 3.786A pdb=" N ASN A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 159 removed outlier: 3.736A pdb=" N ASP A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.565A pdb=" N LEU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 203 removed outlier: 3.930A pdb=" N TYR A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 231 removed outlier: 3.905A pdb=" N HIS A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 241 through 289 removed outlier: 4.281A pdb=" N MET A 247 " --> pdb=" O HIS A 243 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 251 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.608A pdb=" N PHE A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.778A pdb=" N VAL A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.851A pdb=" N LEU A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 removed outlier: 3.524A pdb=" N VAL A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 475 " --> pdb=" O ARG A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 490 through 501 removed outlier: 3.719A pdb=" N LEU A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 509 removed outlier: 4.182A pdb=" N ALA A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 540 removed outlier: 3.858A pdb=" N GLN A 530 " --> pdb=" O PRO A 526 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 removed outlier: 3.545A pdb=" N ILE A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 removed outlier: 3.912A pdb=" N LYS A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 32 removed outlier: 4.194A pdb=" N GLN B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 61 removed outlier: 3.936A pdb=" N THR B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 52 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 75 through 124 removed outlier: 3.877A pdb=" N THR B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 removed outlier: 3.786A pdb=" N ASN B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.736A pdb=" N ASP B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 180 removed outlier: 3.565A pdb=" N LEU B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 203 removed outlier: 3.930A pdb=" N TYR B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 231 removed outlier: 3.905A pdb=" N HIS B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 218 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 241 through 289 removed outlier: 4.281A pdb=" N MET B 247 " --> pdb=" O HIS B 243 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 259 " --> pdb=" O ARG B 255 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.608A pdb=" N PHE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 331 through 353 removed outlier: 3.778A pdb=" N VAL B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 346 " --> pdb=" O HIS B 342 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 349 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.852A pdb=" N LEU B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 removed outlier: 3.524A pdb=" N VAL B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 475 " --> pdb=" O ARG B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 Processing helix chain 'B' and resid 490 through 501 removed outlier: 3.719A pdb=" N LEU B 494 " --> pdb=" O ASP B 490 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 509 removed outlier: 4.182A pdb=" N ALA B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 540 removed outlier: 3.858A pdb=" N GLN B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 531 " --> pdb=" O GLY B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 removed outlier: 3.545A pdb=" N ILE B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.912A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=AA2, first strand: chain 'A' and resid 456 through 458 removed outlier: 7.228A pdb=" N LEU A 457 " --> pdb=" O VAL A 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 408 through 410 Processing sheet with id=AA4, first strand: chain 'B' and resid 456 through 458 removed outlier: 7.227A pdb=" N LEU B 457 " --> pdb=" O VAL B 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 424 hydrogen bonds defined for protein. 1260 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: 2.48 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2872 1.34 - 1.46: 1899 1.46 - 1.57: 4521 1.57 - 1.69: 10 1.69 - 1.81: 66 Bond restraints: 9368 Sorted by residual: bond pdb=" C SER B 302 " pdb=" N PRO B 303 " ideal model delta sigma weight residual 1.336 1.376 -0.040 9.80e-03 1.04e+04 1.64e+01 bond pdb=" C SER A 302 " pdb=" N PRO A 303 " ideal model delta sigma weight residual 1.336 1.375 -0.039 9.80e-03 1.04e+04 1.62e+01 bond pdb=" C LEU B 524 " pdb=" N SER B 525 " ideal model delta sigma weight residual 1.333 1.281 0.052 1.39e-02 5.18e+03 1.41e+01 bond pdb=" C LEU A 524 " pdb=" N SER A 525 " ideal model delta sigma weight residual 1.333 1.281 0.052 1.39e-02 5.18e+03 1.39e+01 bond pdb=" N PHE A 387 " pdb=" CA PHE A 387 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.29e-02 6.01e+03 6.45e+00 ... (remaining 9363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 12164 2.26 - 4.52: 449 4.52 - 6.78: 59 6.78 - 9.05: 24 9.05 - 11.31: 6 Bond angle restraints: 12702 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 132.60 7.27 1.00e+00 1.00e+00 5.28e+01 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 132.63 7.24 1.00e+00 1.00e+00 5.25e+01 angle pdb=" C SER B 307 " pdb=" N THR B 308 " pdb=" CA THR B 308 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C SER A 307 " pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 132.53 4.30 1.00e+00 1.00e+00 1.85e+01 ... (remaining 12697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4813 17.67 - 35.33: 600 35.33 - 53.00: 135 53.00 - 70.66: 40 70.66 - 88.33: 10 Dihedral angle restraints: 5598 sinusoidal: 2316 harmonic: 3282 Sorted by residual: dihedral pdb=" CA MET A 227 " pdb=" C MET A 227 " pdb=" N GLN A 228 " pdb=" CA GLN A 228 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA MET B 227 " pdb=" C MET B 227 " pdb=" N GLN B 228 " pdb=" CA GLN B 228 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ILE A 475 " pdb=" C ILE A 475 " pdb=" N TYR A 476 " pdb=" CA TYR A 476 " ideal model delta harmonic sigma weight residual 180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1017 0.057 - 0.114: 360 0.114 - 0.171: 49 0.171 - 0.228: 18 0.228 - 0.285: 4 Chirality restraints: 1448 Sorted by residual: chirality pdb=" CB ILE A 574 " pdb=" CA ILE A 574 " pdb=" CG1 ILE A 574 " pdb=" CG2 ILE A 574 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE B 574 " pdb=" CA ILE B 574 " pdb=" CG1 ILE B 574 " pdb=" CG2 ILE B 574 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1445 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 167 " -0.055 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 168 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 167 " 0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO B 168 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 291 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO A 292 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.038 5.00e-02 4.00e+02 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1327 2.75 - 3.28: 9119 3.28 - 3.82: 15961 3.82 - 4.36: 19573 4.36 - 4.90: 31882 Nonbonded interactions: 77862 Sorted by model distance: nonbonded pdb=" O THR B 423 " pdb=" O1B ATP B 701 " model vdw 2.206 3.040 nonbonded pdb=" O THR A 423 " pdb=" O1B ATP A 701 " model vdw 2.206 3.040 nonbonded pdb=" O ILE A 291 " pdb=" OG SER A 295 " model vdw 2.312 3.040 nonbonded pdb=" O ILE B 291 " pdb=" OG SER B 295 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR A 108 " pdb=" OE1 GLN B 260 " model vdw 2.316 3.040 ... (remaining 77857 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.720 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 9368 Z= 0.361 Angle : 1.036 11.308 12702 Z= 0.555 Chirality : 0.059 0.285 1448 Planarity : 0.007 0.082 1580 Dihedral : 16.772 88.329 3490 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.19 (0.15), residues: 1122 helix: -4.17 (0.09), residues: 720 sheet: None (None), residues: 0 loop : -3.61 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 520 HIS 0.004 0.001 HIS A 118 PHE 0.032 0.003 PHE A 324 TYR 0.021 0.003 TYR B 319 ARG 0.002 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.26520 ( 424) hydrogen bonds : angle 11.07489 ( 1260) covalent geometry : bond 0.00782 ( 9368) covalent geometry : angle 1.03573 (12702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9050 (mt) cc_final: 0.8779 (mt) REVERT: A 55 PHE cc_start: 0.7354 (t80) cc_final: 0.6893 (m-10) REVERT: A 68 TYR cc_start: 0.7741 (m-80) cc_final: 0.7426 (m-10) REVERT: A 217 LYS cc_start: 0.8455 (tttt) cc_final: 0.8248 (tttp) REVERT: A 247 MET cc_start: 0.7616 (mmt) cc_final: 0.7367 (mmt) REVERT: A 465 PHE cc_start: 0.9099 (m-80) cc_final: 0.8879 (m-10) REVERT: A 567 GLN cc_start: 0.7960 (mp10) cc_final: 0.7664 (pm20) REVERT: B 55 PHE cc_start: 0.7394 (t80) cc_final: 0.6830 (m-10) REVERT: B 315 PHE cc_start: 0.7541 (t80) cc_final: 0.7050 (t80) REVERT: B 388 LEU cc_start: 0.8653 (mt) cc_final: 0.8401 (mt) REVERT: B 422 ASN cc_start: 0.8214 (t0) cc_final: 0.7304 (m-40) REVERT: B 465 PHE cc_start: 0.9070 (m-80) cc_final: 0.8857 (m-10) REVERT: B 495 ARG cc_start: 0.8205 (ttt180) cc_final: 0.7997 (ttt90) REVERT: B 517 ASP cc_start: 0.7162 (m-30) cc_final: 0.6951 (m-30) REVERT: B 518 TRP cc_start: 0.7900 (m-10) cc_final: 0.7481 (m-10) REVERT: B 567 GLN cc_start: 0.7880 (mp10) cc_final: 0.7636 (pm20) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2086 time to fit residues: 79.6867 Evaluate side-chains 198 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN A 201 ASN A 228 GLN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 228 GLN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.102689 restraints weight = 14492.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.106071 restraints weight = 7120.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108216 restraints weight = 4588.365| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9368 Z= 0.157 Angle : 0.698 8.485 12702 Z= 0.359 Chirality : 0.042 0.160 1448 Planarity : 0.006 0.060 1580 Dihedral : 10.029 76.029 1310 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.08 % Allowed : 20.36 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.19), residues: 1122 helix: -2.52 (0.15), residues: 700 sheet: None (None), residues: 0 loop : -3.54 (0.24), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 598 HIS 0.003 0.001 HIS A 342 PHE 0.022 0.002 PHE B 451 TYR 0.013 0.001 TYR A 319 ARG 0.004 0.001 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 424) hydrogen bonds : angle 5.70529 ( 1260) covalent geometry : bond 0.00337 ( 9368) covalent geometry : angle 0.69843 (12702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9097 (mt) cc_final: 0.8867 (mt) REVERT: A 52 LEU cc_start: 0.9376 (tp) cc_final: 0.9009 (tp) REVERT: A 55 PHE cc_start: 0.7526 (t80) cc_final: 0.7039 (m-10) REVERT: A 84 PHE cc_start: 0.7884 (t80) cc_final: 0.7577 (t80) REVERT: A 217 LYS cc_start: 0.8561 (tttt) cc_final: 0.8215 (tttp) REVERT: A 234 GLU cc_start: 0.8615 (tp30) cc_final: 0.8174 (mm-30) REVERT: A 247 MET cc_start: 0.7760 (mmt) cc_final: 0.7519 (mmt) REVERT: A 271 TYR cc_start: 0.9052 (m-10) cc_final: 0.8763 (m-80) REVERT: A 312 LYS cc_start: 0.8231 (tmmt) cc_final: 0.7847 (ptmm) REVERT: A 422 ASN cc_start: 0.8155 (t0) cc_final: 0.7440 (m-40) REVERT: A 518 TRP cc_start: 0.7869 (m-10) cc_final: 0.7629 (m-10) REVERT: B 38 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7320 (tm-30) REVERT: B 51 LEU cc_start: 0.9060 (mt) cc_final: 0.8681 (mp) REVERT: B 55 PHE cc_start: 0.7544 (t80) cc_final: 0.6771 (m-10) REVERT: B 247 MET cc_start: 0.7868 (mmt) cc_final: 0.7649 (mmt) REVERT: B 252 ARG cc_start: 0.8849 (mmt90) cc_final: 0.8637 (mtp85) REVERT: B 312 LYS cc_start: 0.8232 (tmmt) cc_final: 0.7817 (ptmm) REVERT: B 315 PHE cc_start: 0.7693 (t80) cc_final: 0.7136 (t80) REVERT: B 422 ASN cc_start: 0.8079 (t0) cc_final: 0.7642 (m110) REVERT: B 465 PHE cc_start: 0.9071 (m-80) cc_final: 0.8854 (m-10) outliers start: 21 outliers final: 8 residues processed: 239 average time/residue: 0.2581 time to fit residues: 87.3032 Evaluate side-chains 204 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 0.0570 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN ** B 567 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 = 0.3545 r_free = 0.3545 target = 0.129140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.102465 restraints weight = 14723.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105927 restraints weight = 7168.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108066 restraints weight = 4560.950| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9368 Z= 0.143 Angle : 0.638 8.226 12702 Z= 0.327 Chirality : 0.042 0.178 1448 Planarity : 0.004 0.045 1580 Dihedral : 8.537 80.688 1310 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.36 % Allowed : 22.43 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.21), residues: 1122 helix: -1.64 (0.17), residues: 706 sheet: None (None), residues: 0 loop : -3.43 (0.24), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 598 HIS 0.003 0.001 HIS A 226 PHE 0.017 0.002 PHE A 222 TYR 0.011 0.001 TYR A 319 ARG 0.003 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 424) hydrogen bonds : angle 4.97651 ( 1260) covalent geometry : bond 0.00311 ( 9368) covalent geometry : angle 0.63846 (12702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9369 (tp) cc_final: 0.9048 (tp) REVERT: A 55 PHE cc_start: 0.7583 (t80) cc_final: 0.6880 (m-10) REVERT: A 84 PHE cc_start: 0.7925 (t80) cc_final: 0.7675 (t80) REVERT: A 85 LEU cc_start: 0.9223 (tp) cc_final: 0.8973 (tt) REVERT: A 136 ARG cc_start: 0.8308 (mmt-90) cc_final: 0.7783 (mpt180) REVERT: A 217 LYS cc_start: 0.8590 (tttt) cc_final: 0.8302 (tttp) REVERT: A 247 MET cc_start: 0.7811 (mmt) cc_final: 0.7562 (mmt) REVERT: A 268 LEU cc_start: 0.9338 (tt) cc_final: 0.9025 (tp) REVERT: A 312 LYS cc_start: 0.8156 (tmmt) cc_final: 0.7768 (ptmt) REVERT: A 324 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8283 (t80) REVERT: A 422 ASN cc_start: 0.8210 (t0) cc_final: 0.7600 (m110) REVERT: A 502 LEU cc_start: 0.9140 (pt) cc_final: 0.8825 (pp) REVERT: A 561 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7811 (tm-30) REVERT: B 38 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7408 (tm-30) REVERT: B 55 PHE cc_start: 0.7548 (t80) cc_final: 0.6790 (m-10) REVERT: B 85 LEU cc_start: 0.9190 (tp) cc_final: 0.8966 (tt) REVERT: B 312 LYS cc_start: 0.8062 (tmmt) cc_final: 0.7726 (ptmt) REVERT: B 324 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8268 (t80) REVERT: B 422 ASN cc_start: 0.7981 (t0) cc_final: 0.7537 (m-40) REVERT: B 502 LEU cc_start: 0.9116 (pt) cc_final: 0.8800 (pp) REVERT: B 561 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7840 (tm-30) outliers start: 34 outliers final: 17 residues processed: 250 average time/residue: 0.2207 time to fit residues: 78.0194 Evaluate side-chains 214 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 0.0060 chunk 101 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN A 549 GLN ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 215 GLN B 228 GLN B 260 GLN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105200 restraints weight = 14533.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108661 restraints weight = 6947.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110844 restraints weight = 4405.291| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9368 Z= 0.129 Angle : 0.627 7.086 12702 Z= 0.317 Chirality : 0.042 0.161 1448 Planarity : 0.004 0.037 1580 Dihedral : 7.733 78.126 1310 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.75 % Allowed : 23.62 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.22), residues: 1122 helix: -1.16 (0.18), residues: 720 sheet: 0.06 (1.28), residues: 20 loop : -3.47 (0.25), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 598 HIS 0.002 0.001 HIS B 226 PHE 0.015 0.001 PHE A 222 TYR 0.010 0.001 TYR B 271 ARG 0.002 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 424) hydrogen bonds : angle 4.70114 ( 1260) covalent geometry : bond 0.00277 ( 9368) covalent geometry : angle 0.62742 (12702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7714 (tm-30) cc_final: 0.6999 (tm-30) REVERT: A 55 PHE cc_start: 0.7615 (t80) cc_final: 0.6927 (m-10) REVERT: A 84 PHE cc_start: 0.7892 (t80) cc_final: 0.7649 (t80) REVERT: A 85 LEU cc_start: 0.9227 (tp) cc_final: 0.8977 (tt) REVERT: A 136 ARG cc_start: 0.8302 (mmt-90) cc_final: 0.7817 (mpt180) REVERT: A 165 ILE cc_start: 0.8908 (tp) cc_final: 0.8697 (tp) REVERT: A 217 LYS cc_start: 0.8465 (tttt) cc_final: 0.8189 (tttp) REVERT: A 247 MET cc_start: 0.7728 (mmt) cc_final: 0.7427 (mmt) REVERT: A 268 LEU cc_start: 0.9294 (tt) cc_final: 0.9016 (tp) REVERT: A 312 LYS cc_start: 0.8124 (tmmt) cc_final: 0.7786 (ptmm) REVERT: A 324 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8222 (t80) REVERT: A 422 ASN cc_start: 0.8206 (t0) cc_final: 0.7594 (m110) REVERT: A 502 LEU cc_start: 0.9200 (pt) cc_final: 0.8899 (pp) REVERT: B 38 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 55 PHE cc_start: 0.7532 (t80) cc_final: 0.6768 (m-10) REVERT: B 85 LEU cc_start: 0.9208 (tp) cc_final: 0.9003 (tt) REVERT: B 215 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: B 312 LYS cc_start: 0.8099 (tmmt) cc_final: 0.7741 (ptmt) REVERT: B 324 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8237 (t80) REVERT: B 422 ASN cc_start: 0.8021 (t0) cc_final: 0.7539 (m-40) REVERT: B 502 LEU cc_start: 0.9170 (pt) cc_final: 0.8856 (pp) outliers start: 38 outliers final: 23 residues processed: 241 average time/residue: 0.2508 time to fit residues: 90.4942 Evaluate side-chains 224 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105445 restraints weight = 14504.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108888 restraints weight = 6950.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111059 restraints weight = 4425.916| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9368 Z= 0.131 Angle : 0.619 7.927 12702 Z= 0.313 Chirality : 0.041 0.178 1448 Planarity : 0.004 0.035 1580 Dihedral : 7.115 74.060 1310 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.05 % Allowed : 25.49 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.23), residues: 1122 helix: -0.92 (0.18), residues: 718 sheet: 0.18 (1.31), residues: 20 loop : -3.39 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 269 HIS 0.002 0.001 HIS B 226 PHE 0.014 0.001 PHE A 324 TYR 0.009 0.001 TYR A 68 ARG 0.002 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 424) hydrogen bonds : angle 4.54928 ( 1260) covalent geometry : bond 0.00289 ( 9368) covalent geometry : angle 0.61890 (12702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7135 (tm-30) REVERT: A 55 PHE cc_start: 0.7620 (t80) cc_final: 0.6921 (m-10) REVERT: A 85 LEU cc_start: 0.9234 (tp) cc_final: 0.8996 (tt) REVERT: A 136 ARG cc_start: 0.8301 (mmt-90) cc_final: 0.7800 (mpt180) REVERT: A 165 ILE cc_start: 0.8897 (tp) cc_final: 0.8686 (tp) REVERT: A 193 TYR cc_start: 0.8284 (t80) cc_final: 0.7681 (t80) REVERT: A 217 LYS cc_start: 0.8397 (tttt) cc_final: 0.8133 (tttp) REVERT: A 247 MET cc_start: 0.7657 (mmt) cc_final: 0.7366 (mmt) REVERT: A 268 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8986 (tp) REVERT: A 312 LYS cc_start: 0.8034 (tmmt) cc_final: 0.7738 (ptmm) REVERT: A 324 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8228 (t80) REVERT: A 422 ASN cc_start: 0.8200 (t0) cc_final: 0.7571 (m110) REVERT: A 502 LEU cc_start: 0.9203 (pt) cc_final: 0.8922 (pp) REVERT: A 529 MET cc_start: 0.8489 (mtt) cc_final: 0.8037 (mtt) REVERT: A 561 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7833 (tm-30) REVERT: A 567 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7175 (mt0) REVERT: B 55 PHE cc_start: 0.7565 (t80) cc_final: 0.6802 (m-10) REVERT: B 193 TYR cc_start: 0.8232 (t80) cc_final: 0.7601 (t80) REVERT: B 312 LYS cc_start: 0.8116 (tmmt) cc_final: 0.7780 (ptmt) REVERT: B 324 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8266 (t80) REVERT: B 422 ASN cc_start: 0.8021 (t0) cc_final: 0.7529 (m110) REVERT: B 502 LEU cc_start: 0.9178 (pt) cc_final: 0.8900 (pp) REVERT: B 529 MET cc_start: 0.8453 (mtt) cc_final: 0.8010 (mtt) REVERT: B 561 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7852 (tm-30) REVERT: B 567 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7249 (pt0) outliers start: 41 outliers final: 21 residues processed: 242 average time/residue: 0.2271 time to fit residues: 81.4207 Evaluate side-chains 220 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 0 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN ** B 567 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 = 0.3593 r_free = 0.3593 target = 0.132309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.106042 restraints weight = 14550.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109487 restraints weight = 6943.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111663 restraints weight = 4387.724| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9368 Z= 0.130 Angle : 0.625 9.044 12702 Z= 0.313 Chirality : 0.041 0.248 1448 Planarity : 0.004 0.036 1580 Dihedral : 6.712 70.558 1310 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.15 % Allowed : 25.10 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.23), residues: 1122 helix: -0.69 (0.19), residues: 728 sheet: -0.36 (1.20), residues: 20 loop : -3.33 (0.25), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 111 HIS 0.002 0.001 HIS B 226 PHE 0.015 0.001 PHE A 324 TYR 0.010 0.001 TYR B 544 ARG 0.002 0.000 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 424) hydrogen bonds : angle 4.44677 ( 1260) covalent geometry : bond 0.00284 ( 9368) covalent geometry : angle 0.62470 (12702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7744 (tm-30) cc_final: 0.7220 (tm-30) REVERT: A 55 PHE cc_start: 0.7598 (t80) cc_final: 0.6912 (m-10) REVERT: A 85 LEU cc_start: 0.9239 (tp) cc_final: 0.8994 (tt) REVERT: A 136 ARG cc_start: 0.8308 (mmt-90) cc_final: 0.7774 (mpt180) REVERT: A 165 ILE cc_start: 0.8847 (tp) cc_final: 0.8639 (tp) REVERT: A 193 TYR cc_start: 0.8215 (t80) cc_final: 0.7458 (t80) REVERT: A 217 LYS cc_start: 0.8375 (tttt) cc_final: 0.8111 (tttp) REVERT: A 227 MET cc_start: 0.7958 (ptp) cc_final: 0.7562 (ptp) REVERT: A 247 MET cc_start: 0.7701 (mmt) cc_final: 0.7431 (mmt) REVERT: A 268 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9089 (tp) REVERT: A 312 LYS cc_start: 0.8025 (tmmt) cc_final: 0.7737 (ptmm) REVERT: A 324 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8315 (t80) REVERT: A 422 ASN cc_start: 0.8168 (t0) cc_final: 0.7563 (m110) REVERT: A 502 LEU cc_start: 0.9217 (pt) cc_final: 0.8966 (pt) REVERT: A 567 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7150 (mt0) REVERT: B 55 PHE cc_start: 0.7576 (t80) cc_final: 0.6764 (m-10) REVERT: B 136 ARG cc_start: 0.8301 (mmt-90) cc_final: 0.7790 (mpt180) REVERT: B 189 SER cc_start: 0.8402 (t) cc_final: 0.8195 (p) REVERT: B 193 TYR cc_start: 0.8225 (t80) cc_final: 0.7578 (t80) REVERT: B 312 LYS cc_start: 0.8112 (tmmt) cc_final: 0.7754 (ptmm) REVERT: B 324 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8336 (t80) REVERT: B 422 ASN cc_start: 0.8044 (t0) cc_final: 0.7498 (m-40) REVERT: B 502 LEU cc_start: 0.9186 (pt) cc_final: 0.8900 (pp) REVERT: B 528 GLU cc_start: 0.8728 (pm20) cc_final: 0.8395 (pm20) REVERT: B 529 MET cc_start: 0.8465 (mtt) cc_final: 0.8055 (mtt) REVERT: B 567 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7171 (mt0) outliers start: 42 outliers final: 22 residues processed: 239 average time/residue: 0.1911 time to fit residues: 64.9731 Evaluate side-chains 224 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 319 TYR Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 GLN ** B 66 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 = 0.3570 r_free = 0.3570 target = 0.130705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.103936 restraints weight = 14782.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.107348 restraints weight = 7086.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109489 restraints weight = 4501.536| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9368 Z= 0.155 Angle : 0.636 9.306 12702 Z= 0.320 Chirality : 0.042 0.177 1448 Planarity : 0.004 0.038 1580 Dihedral : 6.654 70.059 1310 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.56 % Allowed : 26.09 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.23), residues: 1122 helix: -0.64 (0.19), residues: 726 sheet: -0.79 (1.16), residues: 20 loop : -3.40 (0.25), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 269 HIS 0.003 0.001 HIS B 214 PHE 0.017 0.001 PHE B 84 TYR 0.009 0.001 TYR B 271 ARG 0.004 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 424) hydrogen bonds : angle 4.43933 ( 1260) covalent geometry : bond 0.00351 ( 9368) covalent geometry : angle 0.63633 (12702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7120 (tm-30) REVERT: A 55 PHE cc_start: 0.7612 (t80) cc_final: 0.6921 (m-10) REVERT: A 85 LEU cc_start: 0.9258 (tp) cc_final: 0.9016 (tt) REVERT: A 136 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.7744 (mpt180) REVERT: A 165 ILE cc_start: 0.8871 (tp) cc_final: 0.8643 (tp) REVERT: A 193 TYR cc_start: 0.8278 (t80) cc_final: 0.7530 (t80) REVERT: A 217 LYS cc_start: 0.8380 (tttt) cc_final: 0.8142 (tttp) REVERT: A 227 MET cc_start: 0.7814 (ptp) cc_final: 0.6928 (ptp) REVERT: A 247 MET cc_start: 0.7711 (mmt) cc_final: 0.7460 (mmt) REVERT: A 268 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9117 (tp) REVERT: A 312 LYS cc_start: 0.8050 (tmmt) cc_final: 0.7787 (ptmm) REVERT: A 422 ASN cc_start: 0.8225 (t0) cc_final: 0.7659 (m110) REVERT: A 502 LEU cc_start: 0.9253 (pt) cc_final: 0.8995 (pp) REVERT: A 528 GLU cc_start: 0.8784 (pm20) cc_final: 0.8454 (pm20) REVERT: A 561 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7877 (tm-30) REVERT: A 567 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7096 (mt0) REVERT: B 55 PHE cc_start: 0.7592 (t80) cc_final: 0.6772 (m-10) REVERT: B 83 THR cc_start: 0.8357 (t) cc_final: 0.8102 (t) REVERT: B 85 LEU cc_start: 0.9250 (tp) cc_final: 0.9040 (tt) REVERT: B 136 ARG cc_start: 0.8327 (mmt-90) cc_final: 0.7789 (mpt180) REVERT: B 193 TYR cc_start: 0.8266 (t80) cc_final: 0.7629 (t80) REVERT: B 422 ASN cc_start: 0.8117 (t0) cc_final: 0.7535 (m110) REVERT: B 502 LEU cc_start: 0.9226 (pt) cc_final: 0.8945 (pp) REVERT: B 528 GLU cc_start: 0.8775 (pm20) cc_final: 0.8432 (pm20) REVERT: B 529 MET cc_start: 0.8585 (mtt) cc_final: 0.8112 (mtt) REVERT: B 561 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7905 (tm-30) REVERT: B 567 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7223 (mt0) outliers start: 36 outliers final: 21 residues processed: 236 average time/residue: 0.1952 time to fit residues: 66.6525 Evaluate side-chains 222 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 319 TYR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.131403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105135 restraints weight = 14776.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108589 restraints weight = 6930.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110509 restraints weight = 4346.715| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9368 Z= 0.135 Angle : 0.642 9.742 12702 Z= 0.321 Chirality : 0.042 0.215 1448 Planarity : 0.004 0.037 1580 Dihedral : 6.627 69.977 1310 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.87 % Allowed : 27.47 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.23), residues: 1122 helix: -0.53 (0.19), residues: 728 sheet: -0.86 (1.14), residues: 20 loop : -3.31 (0.25), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 269 HIS 0.002 0.001 HIS B 226 PHE 0.029 0.001 PHE A 324 TYR 0.013 0.001 TYR B 544 ARG 0.003 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 424) hydrogen bonds : angle 4.41263 ( 1260) covalent geometry : bond 0.00300 ( 9368) covalent geometry : angle 0.64169 (12702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 55 PHE cc_start: 0.7603 (t80) cc_final: 0.6899 (m-10) REVERT: A 85 LEU cc_start: 0.9265 (tp) cc_final: 0.9017 (tt) REVERT: A 136 ARG cc_start: 0.8264 (mmt-90) cc_final: 0.7729 (mpt180) REVERT: A 165 ILE cc_start: 0.8878 (tp) cc_final: 0.8657 (tp) REVERT: A 193 TYR cc_start: 0.8166 (t80) cc_final: 0.7259 (t80) REVERT: A 217 LYS cc_start: 0.8364 (tttt) cc_final: 0.8089 (tttp) REVERT: A 247 MET cc_start: 0.7677 (mmt) cc_final: 0.7434 (mmt) REVERT: A 268 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9105 (tp) REVERT: A 422 ASN cc_start: 0.8209 (t0) cc_final: 0.7651 (m110) REVERT: A 502 LEU cc_start: 0.9267 (pt) cc_final: 0.8988 (pp) REVERT: A 528 GLU cc_start: 0.8738 (pm20) cc_final: 0.8313 (pm20) REVERT: A 561 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7903 (tm-30) REVERT: A 567 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7172 (mt0) REVERT: B 38 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 55 PHE cc_start: 0.7577 (t80) cc_final: 0.6766 (m-10) REVERT: B 83 THR cc_start: 0.8317 (t) cc_final: 0.8057 (t) REVERT: B 85 LEU cc_start: 0.9233 (tp) cc_final: 0.9026 (tt) REVERT: B 136 ARG cc_start: 0.8303 (mmt-90) cc_final: 0.7753 (mpt180) REVERT: B 189 SER cc_start: 0.8663 (p) cc_final: 0.8256 (t) REVERT: B 193 TYR cc_start: 0.8164 (t80) cc_final: 0.7359 (t80) REVERT: B 422 ASN cc_start: 0.8119 (t0) cc_final: 0.7533 (m110) REVERT: B 502 LEU cc_start: 0.9205 (pt) cc_final: 0.8956 (pp) REVERT: B 528 GLU cc_start: 0.8773 (pm20) cc_final: 0.8414 (pm20) REVERT: B 529 MET cc_start: 0.8567 (mtt) cc_final: 0.8118 (mtt) REVERT: B 561 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 567 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7193 (mt0) outliers start: 29 outliers final: 23 residues processed: 224 average time/residue: 0.1878 time to fit residues: 61.2956 Evaluate side-chains 222 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 461 GLN B 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106568 restraints weight = 14556.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110069 restraints weight = 6898.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112226 restraints weight = 4343.372| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9368 Z= 0.128 Angle : 0.640 10.273 12702 Z= 0.318 Chirality : 0.042 0.240 1448 Planarity : 0.004 0.036 1580 Dihedral : 6.588 69.730 1310 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.87 % Allowed : 27.67 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.24), residues: 1122 helix: -0.38 (0.19), residues: 724 sheet: -1.03 (1.10), residues: 20 loop : -3.21 (0.25), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 35 HIS 0.002 0.001 HIS A 226 PHE 0.026 0.001 PHE A 324 TYR 0.012 0.001 TYR A 271 ARG 0.003 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 424) hydrogen bonds : angle 4.37247 ( 1260) covalent geometry : bond 0.00279 ( 9368) covalent geometry : angle 0.64048 (12702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 55 PHE cc_start: 0.7595 (t80) cc_final: 0.6901 (m-10) REVERT: A 85 LEU cc_start: 0.9266 (tp) cc_final: 0.9018 (tt) REVERT: A 136 ARG cc_start: 0.8254 (mmt-90) cc_final: 0.7711 (mpt180) REVERT: A 193 TYR cc_start: 0.8155 (t80) cc_final: 0.7225 (t80) REVERT: A 217 LYS cc_start: 0.8356 (tttt) cc_final: 0.8072 (tttp) REVERT: A 247 MET cc_start: 0.7633 (mmt) cc_final: 0.7395 (mmt) REVERT: A 268 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9087 (tp) REVERT: A 280 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8585 (tt) REVERT: A 422 ASN cc_start: 0.8179 (t0) cc_final: 0.7630 (m110) REVERT: A 502 LEU cc_start: 0.9260 (pt) cc_final: 0.8969 (pp) REVERT: A 528 GLU cc_start: 0.8697 (pm20) cc_final: 0.8296 (pm20) REVERT: A 561 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7874 (tm-30) REVERT: A 567 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7129 (mt0) REVERT: B 38 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7648 (tm-30) REVERT: B 55 PHE cc_start: 0.7590 (t80) cc_final: 0.6807 (m-10) REVERT: B 85 LEU cc_start: 0.9230 (tp) cc_final: 0.9026 (tt) REVERT: B 136 ARG cc_start: 0.8282 (mmt-90) cc_final: 0.7741 (mpt180) REVERT: B 193 TYR cc_start: 0.8118 (t80) cc_final: 0.7224 (t80) REVERT: B 215 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8646 (tt0) REVERT: B 234 GLU cc_start: 0.8583 (tp30) cc_final: 0.8337 (tp30) REVERT: B 422 ASN cc_start: 0.8093 (t0) cc_final: 0.7505 (m-40) REVERT: B 502 LEU cc_start: 0.9237 (pt) cc_final: 0.8991 (pt) REVERT: B 528 GLU cc_start: 0.8743 (pm20) cc_final: 0.8402 (pm20) REVERT: B 529 MET cc_start: 0.8553 (mtt) cc_final: 0.8094 (mtt) REVERT: B 561 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 567 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7150 (mt0) outliers start: 29 outliers final: 22 residues processed: 233 average time/residue: 0.1863 time to fit residues: 63.2162 Evaluate side-chains 226 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 71 optimal weight: 0.0470 chunk 82 optimal weight: 1.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106723 restraints weight = 14588.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110190 restraints weight = 6917.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112343 restraints weight = 4352.136| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9368 Z= 0.130 Angle : 0.644 10.276 12702 Z= 0.317 Chirality : 0.042 0.206 1448 Planarity : 0.004 0.035 1580 Dihedral : 6.498 69.201 1310 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.77 % Allowed : 28.26 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.24), residues: 1122 helix: -0.24 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -3.12 (0.24), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 35 HIS 0.002 0.001 HIS B 214 PHE 0.025 0.001 PHE A 324 TYR 0.017 0.001 TYR B 271 ARG 0.004 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 424) hydrogen bonds : angle 4.32405 ( 1260) covalent geometry : bond 0.00288 ( 9368) covalent geometry : angle 0.64355 (12702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 55 PHE cc_start: 0.7589 (t80) cc_final: 0.6897 (m-10) REVERT: A 85 LEU cc_start: 0.9277 (tp) cc_final: 0.9032 (tt) REVERT: A 136 ARG cc_start: 0.8229 (mmt-90) cc_final: 0.7707 (mpt180) REVERT: A 189 SER cc_start: 0.8357 (p) cc_final: 0.7975 (t) REVERT: A 193 TYR cc_start: 0.8106 (t80) cc_final: 0.7206 (t80) REVERT: A 217 LYS cc_start: 0.8344 (tttt) cc_final: 0.8077 (tttp) REVERT: A 247 MET cc_start: 0.7629 (mmt) cc_final: 0.7398 (mmt) REVERT: A 268 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9083 (tp) REVERT: A 280 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8555 (tt) REVERT: A 422 ASN cc_start: 0.8203 (t0) cc_final: 0.7584 (m110) REVERT: A 502 LEU cc_start: 0.9245 (pt) cc_final: 0.8957 (pp) REVERT: A 528 GLU cc_start: 0.8687 (pm20) cc_final: 0.8273 (pm20) REVERT: A 561 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 567 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7113 (mt0) REVERT: B 38 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 55 PHE cc_start: 0.7588 (t80) cc_final: 0.6803 (m-10) REVERT: B 85 LEU cc_start: 0.9244 (tp) cc_final: 0.9035 (tt) REVERT: B 136 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.7739 (mpt180) REVERT: B 152 ARG cc_start: 0.8507 (ttm170) cc_final: 0.8048 (mtm180) REVERT: B 193 TYR cc_start: 0.8088 (t80) cc_final: 0.7123 (t80) REVERT: B 234 GLU cc_start: 0.8577 (tp30) cc_final: 0.8325 (tp30) REVERT: B 293 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7172 (tt) REVERT: B 422 ASN cc_start: 0.8101 (t0) cc_final: 0.7499 (m-40) REVERT: B 502 LEU cc_start: 0.9226 (pt) cc_final: 0.8953 (pp) REVERT: B 528 GLU cc_start: 0.8741 (pm20) cc_final: 0.8385 (pm20) REVERT: B 529 MET cc_start: 0.8556 (mtt) cc_final: 0.8115 (mtt) REVERT: B 561 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 567 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7145 (mt0) outliers start: 28 outliers final: 22 residues processed: 231 average time/residue: 0.1802 time to fit residues: 60.2230 Evaluate side-chains 224 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 99 optimal weight: 0.3980 chunk 55 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN A 549 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.135764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.110083 restraints weight = 14459.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113590 restraints weight = 6800.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115741 restraints weight = 4258.129| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9368 Z= 0.119 Angle : 0.638 10.276 12702 Z= 0.314 Chirality : 0.041 0.182 1448 Planarity : 0.004 0.034 1580 Dihedral : 6.412 65.359 1310 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.87 % Allowed : 28.66 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.24), residues: 1122 helix: -0.11 (0.19), residues: 724 sheet: -1.22 (1.07), residues: 20 loop : -3.00 (0.26), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 598 HIS 0.003 0.001 HIS A 226 PHE 0.023 0.001 PHE A 324 TYR 0.020 0.001 TYR B 544 ARG 0.003 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 424) hydrogen bonds : angle 4.25903 ( 1260) covalent geometry : bond 0.00255 ( 9368) covalent geometry : angle 0.63809 (12702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3120.40 seconds wall clock time: 57 minutes 35.41 seconds (3455.41 seconds total)