Starting phenix.real_space_refine on Fri Mar 14 01:52:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rvx_10016/03_2025/6rvx_10016.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rvx_10016/03_2025/6rvx_10016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rvx_10016/03_2025/6rvx_10016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rvx_10016/03_2025/6rvx_10016.map" model { file = "/net/cci-nas-00/data/ceres_data/6rvx_10016/03_2025/6rvx_10016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rvx_10016/03_2025/6rvx_10016.cif" } resolution = 3.61 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= 0.001 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 6300 2.51 5 N 1602 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9627 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3209 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 16, 'TRANS': 413} Chain breaks: 1 Restraints were copied for chains: C, B Time building chain proxies: 5.59, per 1000 atoms: 0.58 Number of scatterers: 9627 At special positions: 0 Unit cell: (117.392, 120.428, 81.972, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1680 8.00 N 1602 7.00 C 6300 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: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2334 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 69.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.611A pdb=" N ALA A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.321A pdb=" N SER A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ALA A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 117 removed outlier: 4.185A pdb=" N LEU A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.809A pdb=" N VAL A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 128 through 153 Processing helix chain 'A' and resid 184 through 192 removed outlier: 4.047A pdb=" N ASN A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 248 removed outlier: 3.812A pdb=" N VAL A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.800A pdb=" N ILE A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 292 removed outlier: 3.986A pdb=" N VAL A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Proline residue: A 278 - end of helix removed outlier: 3.781A pdb=" N MET A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 320 Processing helix chain 'A' and resid 320 through 329 removed outlier: 3.840A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 340 removed outlier: 3.949A pdb=" N PHE A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 356 through 367 removed outlier: 4.288A pdb=" N GLU A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN A 367 " --> pdb=" O CYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 410 through 423 removed outlier: 3.980A pdb=" N ILE A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 445 removed outlier: 3.675A pdb=" N LEU A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.877A pdb=" N HIS A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER A 454 " --> pdb=" O ASP A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 483 removed outlier: 3.803A pdb=" N VAL A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 74 removed outlier: 3.611A pdb=" N ALA B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 removed outlier: 4.321A pdb=" N SER B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 117 removed outlier: 4.184A pdb=" N LEU B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Proline residue: B 106 - end of helix removed outlier: 3.810A pdb=" N VAL B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 128 through 153 Processing helix chain 'B' and resid 184 through 192 removed outlier: 4.047A pdb=" N ASN B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 248 removed outlier: 3.814A pdb=" N VAL B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.800A pdb=" N ILE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 292 removed outlier: 3.987A pdb=" N VAL B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.780A pdb=" N MET B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 320 Processing helix chain 'B' and resid 320 through 329 removed outlier: 3.839A pdb=" N PHE B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.950A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 356 through 367 removed outlier: 4.288A pdb=" N GLU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN B 367 " --> pdb=" O CYS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 397 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 410 through 423 removed outlier: 3.981A pdb=" N ILE B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 445 removed outlier: 3.675A pdb=" N LEU B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.877A pdb=" N HIS B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER B 454 " --> pdb=" O ASP B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 483 removed outlier: 3.803A pdb=" N VAL B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 74 removed outlier: 3.610A pdb=" N ALA C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 removed outlier: 4.321A pdb=" N SER C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ALA C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 117 removed outlier: 4.186A pdb=" N LEU C 97 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Proline residue: C 106 - end of helix removed outlier: 3.810A pdb=" N VAL C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 128 through 153 Processing helix chain 'C' and resid 184 through 192 removed outlier: 4.047A pdb=" N ASN C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 248 removed outlier: 3.813A pdb=" N VAL C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.800A pdb=" N ILE C 256 " --> pdb=" O GLY C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 292 removed outlier: 3.987A pdb=" N VAL C 268 " --> pdb=" O GLU C 264 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 3.780A pdb=" N MET C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 320 Processing helix chain 'C' and resid 320 through 329 removed outlier: 3.839A pdb=" N PHE C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 340 removed outlier: 3.950A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 356 through 367 removed outlier: 4.288A pdb=" N GLU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU C 366 " --> pdb=" O LYS C 362 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 367 " --> pdb=" O CYS C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 410 through 423 removed outlier: 3.980A pdb=" N ILE C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 445 removed outlier: 3.674A pdb=" N LEU C 439 " --> pdb=" O GLY C 435 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 442 " --> pdb=" O THR C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 removed outlier: 3.876A pdb=" N HIS C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER C 454 " --> pdb=" O ASP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 483 removed outlier: 3.803A pdb=" N VAL C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 210 removed outlier: 3.659A pdb=" N VAL A 220 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 210 removed outlier: 3.659A pdb=" N VAL B 220 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 210 removed outlier: 3.658A pdb=" N VAL C 220 " --> pdb=" O GLU C 209 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1611 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: 2.75 Time building geometry restraints manager: 2.61 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: 2892 1.34 - 1.46: 1438 1.46 - 1.57: 5396 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9798 Sorted by residual: bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.50e+00 bond pdb=" CG1 ILE C 273 " pdb=" CD1 ILE C 273 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.48e+00 bond pdb=" CG1 ILE A 273 " pdb=" CD1 ILE A 273 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.44e+00 bond pdb=" CG LEU A 112 " pdb=" CD1 LEU A 112 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 bond pdb=" CG LEU C 112 " pdb=" CD1 LEU C 112 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.07e+00 ... (remaining 9793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 12672 2.00 - 4.00: 535 4.00 - 6.00: 98 6.00 - 7.99: 30 7.99 - 9.99: 9 Bond angle restraints: 13344 Sorted by residual: angle pdb=" N VAL A 197 " pdb=" CA VAL A 197 " pdb=" C VAL A 197 " ideal model delta sigma weight residual 112.96 107.26 5.70 1.00e+00 1.00e+00 3.25e+01 angle pdb=" N VAL C 197 " pdb=" CA VAL C 197 " pdb=" C VAL C 197 " ideal model delta sigma weight residual 112.96 107.26 5.70 1.00e+00 1.00e+00 3.24e+01 angle pdb=" N VAL B 197 " pdb=" CA VAL B 197 " pdb=" C VAL B 197 " ideal model delta sigma weight residual 112.96 107.30 5.66 1.00e+00 1.00e+00 3.20e+01 angle pdb=" N ILE B 456 " pdb=" CA ILE B 456 " pdb=" C ILE B 456 " ideal model delta sigma weight residual 111.90 107.84 4.06 8.10e-01 1.52e+00 2.51e+01 angle pdb=" N ILE A 456 " pdb=" CA ILE A 456 " pdb=" C ILE A 456 " ideal model delta sigma weight residual 111.90 107.86 4.04 8.10e-01 1.52e+00 2.49e+01 ... (remaining 13339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.69: 4846 13.69 - 27.38: 689 27.38 - 41.07: 195 41.07 - 54.76: 27 54.76 - 68.45: 9 Dihedral angle restraints: 5766 sinusoidal: 2127 harmonic: 3639 Sorted by residual: dihedral pdb=" CA THR B 416 " pdb=" C THR B 416 " pdb=" N ILE B 417 " pdb=" CA ILE B 417 " ideal model delta harmonic sigma weight residual 180.00 156.57 23.43 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA THR C 416 " pdb=" C THR C 416 " pdb=" N ILE C 417 " pdb=" CA ILE C 417 " ideal model delta harmonic sigma weight residual 180.00 156.59 23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA THR A 416 " pdb=" C THR A 416 " pdb=" N ILE A 417 " pdb=" CA ILE A 417 " ideal model delta harmonic sigma weight residual 180.00 156.63 23.37 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 5763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1411 0.070 - 0.140: 218 0.140 - 0.210: 30 0.210 - 0.280: 6 0.280 - 0.350: 3 Chirality restraints: 1668 Sorted by residual: chirality pdb=" CB VAL B 90 " pdb=" CA VAL B 90 " pdb=" CG1 VAL B 90 " pdb=" CG2 VAL B 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB VAL C 90 " pdb=" CA VAL C 90 " pdb=" CG1 VAL C 90 " pdb=" CG2 VAL C 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB VAL A 90 " pdb=" CA VAL A 90 " pdb=" CG1 VAL A 90 " pdb=" CG2 VAL A 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 1665 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 277 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.10e+01 pdb=" N PRO C 278 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 278 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 278 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 277 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO B 278 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 278 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 278 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 277 " 0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO A 278 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 278 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 278 " 0.046 5.00e-02 4.00e+02 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2391 2.79 - 3.32: 8551 3.32 - 3.84: 15658 3.84 - 4.37: 17932 4.37 - 4.90: 31395 Nonbonded interactions: 75927 Sorted by model distance: nonbonded pdb=" O GLY A 434 " pdb=" OG1 THR A 438 " model vdw 2.261 3.040 nonbonded pdb=" O GLY C 434 " pdb=" OG1 THR C 438 " model vdw 2.261 3.040 nonbonded pdb=" O GLY B 434 " pdb=" OG1 THR B 438 " model vdw 2.262 3.040 nonbonded pdb=" O SER B 198 " pdb=" OG SER B 198 " model vdw 2.323 3.040 nonbonded pdb=" O SER A 198 " pdb=" OG SER A 198 " model vdw 2.323 3.040 ... (remaining 75922 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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: 0.610 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.570 Find NCS groups from input model: 0.190 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.006 0.062 9798 Z= 0.398 Angle : 0.986 9.992 13344 Z= 0.541 Chirality : 0.055 0.350 1668 Planarity : 0.008 0.083 1656 Dihedral : 14.073 68.451 3432 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.29 % Allowed : 7.94 % Favored : 91.76 % 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: -5.46 (0.16), residues: 1278 helix: -3.44 (0.11), residues: 942 sheet: -3.34 (0.67), residues: 30 loop : -3.32 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 461 HIS 0.003 0.001 HIS A 373 PHE 0.018 0.002 PHE A 91 TYR 0.009 0.002 TYR B 334 ARG 0.002 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 1.058 Fit side-chains REVERT: A 260 ASN cc_start: 0.7464 (t0) cc_final: 0.7097 (t0) REVERT: A 267 MET cc_start: 0.7049 (mmt) cc_final: 0.6733 (mmm) REVERT: A 417 ILE cc_start: 0.8505 (tp) cc_final: 0.8110 (tt) REVERT: A 457 LEU cc_start: 0.8871 (tp) cc_final: 0.8584 (tp) REVERT: B 260 ASN cc_start: 0.7328 (t0) cc_final: 0.6888 (t0) REVERT: B 411 PHE cc_start: 0.8175 (t80) cc_final: 0.7826 (t80) REVERT: B 417 ILE cc_start: 0.8732 (tp) cc_final: 0.8270 (tt) REVERT: C 52 ASN cc_start: 0.8828 (p0) cc_final: 0.8316 (p0) REVERT: C 260 ASN cc_start: 0.7405 (t0) cc_final: 0.6987 (t0) REVERT: C 411 PHE cc_start: 0.8164 (t80) cc_final: 0.7920 (t80) REVERT: C 417 ILE cc_start: 0.8570 (tp) cc_final: 0.8120 (tt) outliers start: 3 outliers final: 0 residues processed: 153 average time/residue: 0.2453 time to fit residues: 51.7225 Evaluate side-chains 118 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS A 386 ASN B 313 HIS B 386 ASN C 313 HIS C 386 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.159991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.124973 restraints weight = 10669.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.125366 restraints weight = 18780.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.126580 restraints weight = 15845.848| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9798 Z= 0.180 Angle : 0.613 7.875 13344 Z= 0.319 Chirality : 0.039 0.159 1668 Planarity : 0.006 0.066 1656 Dihedral : 5.510 19.394 1365 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.47 % Allowed : 12.06 % Favored : 86.47 % 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: -3.41 (0.21), residues: 1278 helix: -1.74 (0.15), residues: 933 sheet: -3.34 (0.65), residues: 36 loop : -3.20 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 461 HIS 0.001 0.000 HIS A 373 PHE 0.022 0.001 PHE C 326 TYR 0.010 0.001 TYR C 208 ARG 0.004 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.856 Fit side-chains REVERT: A 126 ARG cc_start: 0.6442 (mmt90) cc_final: 0.6094 (tmm160) REVERT: A 208 TYR cc_start: 0.8169 (m-80) cc_final: 0.7293 (m-80) REVERT: A 229 MET cc_start: 0.8134 (ptp) cc_final: 0.7794 (ptp) REVERT: A 260 ASN cc_start: 0.7459 (t0) cc_final: 0.7095 (t0) REVERT: A 307 LEU cc_start: 0.8514 (tp) cc_final: 0.8212 (tt) REVERT: A 417 ILE cc_start: 0.8131 (tp) cc_final: 0.7860 (tt) REVERT: A 457 LEU cc_start: 0.8807 (tp) cc_final: 0.8554 (tp) REVERT: A 465 ARG cc_start: 0.7683 (mmt-90) cc_final: 0.7391 (mmt90) REVERT: B 260 ASN cc_start: 0.7455 (t0) cc_final: 0.7076 (t0) REVERT: B 417 ILE cc_start: 0.8370 (tp) cc_final: 0.8045 (tt) REVERT: C 126 ARG cc_start: 0.6387 (mmt90) cc_final: 0.6109 (tpt-90) REVERT: C 208 TYR cc_start: 0.8310 (m-80) cc_final: 0.8013 (m-10) REVERT: C 260 ASN cc_start: 0.7376 (t0) cc_final: 0.6902 (t0) REVERT: C 267 MET cc_start: 0.7476 (mmm) cc_final: 0.7047 (mmt) REVERT: C 417 ILE cc_start: 0.8179 (tp) cc_final: 0.7880 (tt) outliers start: 15 outliers final: 8 residues processed: 157 average time/residue: 0.2161 time to fit residues: 48.7656 Evaluate side-chains 138 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain C residue 422 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 0.0470 chunk 117 optimal weight: 0.0570 chunk 109 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.161872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.128780 restraints weight = 10734.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.127068 restraints weight = 18665.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.128625 restraints weight = 16511.368| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9798 Z= 0.147 Angle : 0.601 9.837 13344 Z= 0.302 Chirality : 0.039 0.175 1668 Planarity : 0.005 0.061 1656 Dihedral : 4.980 19.449 1365 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.45 % Allowed : 15.10 % Favored : 82.45 % 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: -2.30 (0.23), residues: 1278 helix: -0.86 (0.17), residues: 918 sheet: -2.98 (0.69), residues: 36 loop : -2.94 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 461 HIS 0.001 0.000 HIS A 373 PHE 0.022 0.001 PHE C 326 TYR 0.007 0.001 TYR C 208 ARG 0.003 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.893 Fit side-chains REVERT: A 126 ARG cc_start: 0.6342 (mmt90) cc_final: 0.6138 (tmm160) REVERT: A 208 TYR cc_start: 0.7993 (m-80) cc_final: 0.7120 (m-80) REVERT: A 394 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8188 (mp-120) REVERT: A 417 ILE cc_start: 0.8184 (tp) cc_final: 0.7959 (tt) REVERT: A 437 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7942 (tt) REVERT: A 465 ARG cc_start: 0.7797 (mmt-90) cc_final: 0.7470 (mmt90) REVERT: B 85 ARG cc_start: 0.5666 (ttt180) cc_final: 0.5337 (ttt180) REVERT: B 126 ARG cc_start: 0.7545 (tpt170) cc_final: 0.7125 (tpt-90) REVERT: B 260 ASN cc_start: 0.7386 (t0) cc_final: 0.7124 (t0) REVERT: B 387 MET cc_start: 0.7823 (mtp) cc_final: 0.7173 (mtp) REVERT: B 394 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.7010 (mp-120) REVERT: B 417 ILE cc_start: 0.8366 (tp) cc_final: 0.8120 (tt) REVERT: C 260 ASN cc_start: 0.7371 (t0) cc_final: 0.7170 (t0) REVERT: C 394 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7591 (mp-120) REVERT: C 417 ILE cc_start: 0.8114 (tp) cc_final: 0.7880 (tt) outliers start: 25 outliers final: 11 residues processed: 174 average time/residue: 0.1819 time to fit residues: 45.8679 Evaluate side-chains 152 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 422 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 59 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 0.2980 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 HIS ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 HIS C 316 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.160662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.126656 restraints weight = 10552.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.124770 restraints weight = 18946.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.126220 restraints weight = 16860.617| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9798 Z= 0.174 Angle : 0.616 9.489 13344 Z= 0.306 Chirality : 0.040 0.186 1668 Planarity : 0.005 0.059 1656 Dihedral : 4.792 19.264 1365 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.94 % Allowed : 16.37 % Favored : 80.69 % 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: -1.79 (0.24), residues: 1278 helix: -0.45 (0.18), residues: 912 sheet: -2.71 (0.71), residues: 36 loop : -2.86 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 461 HIS 0.001 0.000 HIS B 373 PHE 0.022 0.001 PHE C 326 TYR 0.011 0.001 TYR C 208 ARG 0.002 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.000 Fit side-chains REVERT: A 126 ARG cc_start: 0.6360 (mmt90) cc_final: 0.6138 (tmm160) REVERT: A 208 TYR cc_start: 0.7997 (m-80) cc_final: 0.7148 (m-80) REVERT: A 229 MET cc_start: 0.8086 (ptp) cc_final: 0.7771 (ptp) REVERT: A 394 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8134 (mp-120) REVERT: A 417 ILE cc_start: 0.8236 (tp) cc_final: 0.7927 (tt) REVERT: B 126 ARG cc_start: 0.7339 (tpt170) cc_final: 0.7032 (tpt-90) REVERT: B 186 ASP cc_start: 0.8182 (t70) cc_final: 0.7963 (t70) REVERT: B 260 ASN cc_start: 0.7401 (t0) cc_final: 0.7131 (t0) REVERT: B 394 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7018 (mp-120) REVERT: C 52 ASN cc_start: 0.8614 (p0) cc_final: 0.8298 (p0) REVERT: C 260 ASN cc_start: 0.7411 (t0) cc_final: 0.7178 (t0) REVERT: C 394 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7604 (mp-120) REVERT: C 417 ILE cc_start: 0.8194 (tp) cc_final: 0.7992 (tt) outliers start: 30 outliers final: 13 residues processed: 160 average time/residue: 0.1896 time to fit residues: 43.9388 Evaluate side-chains 149 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 422 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 51 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 23 optimal weight: 0.0040 chunk 119 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 82 optimal weight: 0.0020 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN C 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.162927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.129829 restraints weight = 10483.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.128094 restraints weight = 17992.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.129181 restraints weight = 17321.355| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9798 Z= 0.151 Angle : 0.598 9.534 13344 Z= 0.297 Chirality : 0.040 0.182 1668 Planarity : 0.005 0.060 1656 Dihedral : 4.554 18.664 1365 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.65 % Allowed : 16.18 % Favored : 81.18 % 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: -1.41 (0.25), residues: 1278 helix: -0.12 (0.18), residues: 906 sheet: -2.45 (0.73), residues: 36 loop : -2.84 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 461 HIS 0.001 0.000 HIS B 373 PHE 0.024 0.001 PHE C 326 TYR 0.010 0.001 TYR C 208 ARG 0.002 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.073 Fit side-chains REVERT: A 126 ARG cc_start: 0.6402 (mmt90) cc_final: 0.6125 (tmm160) REVERT: A 208 TYR cc_start: 0.7933 (m-80) cc_final: 0.7115 (m-80) REVERT: A 394 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8165 (mp-120) REVERT: A 417 ILE cc_start: 0.8148 (tp) cc_final: 0.7883 (tt) REVERT: B 126 ARG cc_start: 0.7323 (tpt170) cc_final: 0.7080 (tpt-90) REVERT: B 260 ASN cc_start: 0.7486 (t0) cc_final: 0.7201 (t0) REVERT: B 394 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.6989 (mp-120) REVERT: B 437 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7908 (tt) REVERT: C 52 ASN cc_start: 0.8560 (p0) cc_final: 0.8301 (p0) REVERT: C 260 ASN cc_start: 0.7370 (t0) cc_final: 0.7107 (t0) REVERT: C 394 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7544 (mp-120) outliers start: 27 outliers final: 10 residues processed: 169 average time/residue: 0.1968 time to fit residues: 47.3160 Evaluate side-chains 149 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 422 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 66 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.162184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.125413 restraints weight = 10574.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.123922 restraints weight = 16676.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.125309 restraints weight = 15808.268| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9798 Z= 0.173 Angle : 0.619 9.144 13344 Z= 0.305 Chirality : 0.040 0.171 1668 Planarity : 0.004 0.060 1656 Dihedral : 4.528 18.770 1365 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.94 % Allowed : 16.86 % Favored : 80.20 % 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: -1.18 (0.25), residues: 1278 helix: 0.07 (0.18), residues: 903 sheet: -2.24 (0.74), residues: 36 loop : -2.82 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 461 HIS 0.001 0.000 HIS B 373 PHE 0.025 0.001 PHE C 326 TYR 0.008 0.001 TYR C 208 ARG 0.003 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.931 Fit side-chains REVERT: A 126 ARG cc_start: 0.6474 (mmt90) cc_final: 0.6083 (tmm160) REVERT: A 208 TYR cc_start: 0.7940 (m-80) cc_final: 0.7098 (m-80) REVERT: A 229 MET cc_start: 0.8135 (ptp) cc_final: 0.7824 (ptp) REVERT: A 394 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8127 (mp-120) REVERT: A 417 ILE cc_start: 0.8112 (tp) cc_final: 0.7870 (tt) REVERT: B 126 ARG cc_start: 0.7298 (tpt170) cc_final: 0.7020 (tpt-90) REVERT: B 186 ASP cc_start: 0.8169 (t70) cc_final: 0.7938 (t70) REVERT: B 260 ASN cc_start: 0.7541 (t0) cc_final: 0.7190 (t0) REVERT: B 394 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.6970 (mp-120) REVERT: C 52 ASN cc_start: 0.8583 (p0) cc_final: 0.8344 (p0) REVERT: C 260 ASN cc_start: 0.7453 (t0) cc_final: 0.7170 (t0) REVERT: C 394 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7506 (mp-120) outliers start: 30 outliers final: 19 residues processed: 154 average time/residue: 0.1958 time to fit residues: 44.0242 Evaluate side-chains 145 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 422 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 90 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 23 optimal weight: 0.0070 chunk 79 optimal weight: 0.0170 chunk 86 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.164195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.128130 restraints weight = 10494.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.126912 restraints weight = 15157.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128232 restraints weight = 14925.222| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9798 Z= 0.158 Angle : 0.611 8.685 13344 Z= 0.300 Chirality : 0.040 0.183 1668 Planarity : 0.004 0.060 1656 Dihedral : 4.360 17.132 1365 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.94 % Allowed : 17.35 % Favored : 79.71 % 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: -0.99 (0.25), residues: 1278 helix: 0.19 (0.19), residues: 909 sheet: -2.19 (0.73), residues: 36 loop : -2.74 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 461 HIS 0.001 0.000 HIS B 373 PHE 0.025 0.001 PHE C 326 TYR 0.009 0.001 TYR C 208 ARG 0.002 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.905 Fit side-chains REVERT: A 126 ARG cc_start: 0.6514 (mmt90) cc_final: 0.6013 (tmm160) REVERT: A 208 TYR cc_start: 0.7884 (m-80) cc_final: 0.7074 (m-80) REVERT: A 394 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8101 (mp-120) REVERT: A 417 ILE cc_start: 0.8025 (tp) cc_final: 0.7812 (tt) REVERT: B 126 ARG cc_start: 0.7395 (tpt170) cc_final: 0.7091 (tpt-90) REVERT: B 186 ASP cc_start: 0.8114 (t70) cc_final: 0.7883 (t70) REVERT: B 394 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.6965 (mp-120) REVERT: B 437 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7850 (tt) REVERT: C 394 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7452 (mp-120) outliers start: 30 outliers final: 19 residues processed: 158 average time/residue: 0.1857 time to fit residues: 43.1119 Evaluate side-chains 149 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 422 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.155763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 131)---------------| | r_work = 0.3215 r_free = 0.3215 target = 0.117980 restraints weight = 10767.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.108870 restraints weight = 17061.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.108043 restraints weight = 16051.523| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9798 Z= 0.321 Angle : 0.700 8.158 13344 Z= 0.342 Chirality : 0.046 0.319 1668 Planarity : 0.005 0.064 1656 Dihedral : 4.861 20.047 1365 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.55 % Allowed : 18.53 % Favored : 78.92 % 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: -1.31 (0.24), residues: 1278 helix: -0.09 (0.18), residues: 909 sheet: -2.29 (0.70), residues: 36 loop : -2.71 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.001 0.000 HIS B 373 PHE 0.026 0.002 PHE C 326 TYR 0.007 0.001 TYR C 208 ARG 0.003 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.957 Fit side-chains REVERT: A 126 ARG cc_start: 0.6546 (mmt90) cc_final: 0.6126 (tpt-90) REVERT: A 208 TYR cc_start: 0.8043 (m-80) cc_final: 0.7117 (m-80) REVERT: A 394 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8031 (mp-120) REVERT: A 417 ILE cc_start: 0.8126 (tp) cc_final: 0.7895 (tt) REVERT: B 85 ARG cc_start: 0.5713 (ttt180) cc_final: 0.5475 (ttt180) REVERT: B 126 ARG cc_start: 0.7222 (tpt170) cc_final: 0.6852 (tpt-90) REVERT: B 186 ASP cc_start: 0.8177 (t70) cc_final: 0.7970 (t70) REVERT: B 260 ASN cc_start: 0.7629 (t0) cc_final: 0.7189 (t0) REVERT: B 394 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.6980 (mp-120) REVERT: C 52 ASN cc_start: 0.8729 (p0) cc_final: 0.8342 (p0) REVERT: C 260 ASN cc_start: 0.7592 (t0) cc_final: 0.7175 (t0) REVERT: C 394 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7732 (mp-120) outliers start: 26 outliers final: 17 residues processed: 149 average time/residue: 0.1908 time to fit residues: 41.5997 Evaluate side-chains 145 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 422 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 30 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 4 optimal weight: 0.0270 chunk 69 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.160055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.125764 restraints weight = 10572.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.123317 restraints weight = 19855.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.124862 restraints weight = 16497.934| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9798 Z= 0.181 Angle : 0.637 8.185 13344 Z= 0.311 Chirality : 0.042 0.246 1668 Planarity : 0.004 0.062 1656 Dihedral : 4.588 17.276 1365 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.35 % Allowed : 19.90 % Favored : 77.75 % 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: -1.04 (0.25), residues: 1278 helix: 0.09 (0.18), residues: 918 sheet: -2.24 (0.68), residues: 36 loop : -2.56 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 461 HIS 0.001 0.000 HIS C 373 PHE 0.026 0.001 PHE C 326 TYR 0.009 0.001 TYR C 208 ARG 0.002 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.150 Fit side-chains REVERT: A 208 TYR cc_start: 0.7881 (m-80) cc_final: 0.7042 (m-80) REVERT: A 394 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8122 (mp-120) REVERT: A 417 ILE cc_start: 0.8175 (tp) cc_final: 0.7952 (tt) REVERT: B 126 ARG cc_start: 0.7233 (tpt170) cc_final: 0.6878 (tpt-90) REVERT: B 394 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7031 (mp-120) REVERT: C 394 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7611 (mp-120) outliers start: 24 outliers final: 17 residues processed: 146 average time/residue: 0.2362 time to fit residues: 50.3859 Evaluate side-chains 140 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 422 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 35 optimal weight: 0.0770 chunk 76 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.163143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.127394 restraints weight = 10555.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.125542 restraints weight = 18526.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.126931 restraints weight = 17838.307| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9798 Z= 0.169 Angle : 0.630 8.572 13344 Z= 0.307 Chirality : 0.042 0.311 1668 Planarity : 0.004 0.058 1656 Dihedral : 4.385 16.881 1365 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.06 % Allowed : 20.88 % Favored : 77.06 % 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: -0.82 (0.25), residues: 1278 helix: 0.26 (0.19), residues: 918 sheet: -2.11 (0.68), residues: 36 loop : -2.55 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 461 HIS 0.001 0.000 HIS B 373 PHE 0.027 0.001 PHE C 326 TYR 0.011 0.001 TYR C 208 ARG 0.002 0.000 ARG C 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.659 Fit side-chains REVERT: A 126 ARG cc_start: 0.7291 (tpt-90) cc_final: 0.5597 (tmm160) REVERT: A 208 TYR cc_start: 0.7841 (m-80) cc_final: 0.6982 (m-80) REVERT: A 222 VAL cc_start: 0.8532 (p) cc_final: 0.8290 (m) REVERT: A 394 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8174 (mp-120) REVERT: B 126 ARG cc_start: 0.7322 (tpt170) cc_final: 0.6953 (tpt-90) REVERT: B 186 ASP cc_start: 0.8130 (t70) cc_final: 0.7904 (t70) REVERT: B 326 PHE cc_start: 0.7260 (t80) cc_final: 0.7052 (t80) REVERT: B 394 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7010 (mp-120) REVERT: C 325 TYR cc_start: 0.7864 (t80) cc_final: 0.7599 (t80) REVERT: C 394 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7559 (mp-120) outliers start: 21 outliers final: 17 residues processed: 138 average time/residue: 0.2161 time to fit residues: 44.0302 Evaluate side-chains 134 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 422 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 18 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.162262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.129202 restraints weight = 10576.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.127446 restraints weight = 19943.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.128700 restraints weight = 18492.784| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9798 Z= 0.186 Angle : 0.634 8.453 13344 Z= 0.310 Chirality : 0.042 0.316 1668 Planarity : 0.004 0.057 1656 Dihedral : 4.399 17.729 1365 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.16 % Allowed : 21.47 % Favored : 76.37 % 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: -0.72 (0.25), residues: 1278 helix: 0.30 (0.19), residues: 918 sheet: -1.34 (0.70), residues: 42 loop : -2.50 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 461 HIS 0.001 0.000 HIS B 373 PHE 0.027 0.001 PHE C 326 TYR 0.011 0.001 TYR C 208 ARG 0.004 0.000 ARG A 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3077.33 seconds wall clock time: 56 minutes 12.29 seconds (3372.29 seconds total)