Starting phenix.real_space_refine on Wed Feb 4 16:06:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ps4_71822/02_2026/9ps4_71822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ps4_71822/02_2026/9ps4_71822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ps4_71822/02_2026/9ps4_71822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ps4_71822/02_2026/9ps4_71822.map" model { file = "/net/cci-nas-00/data/ceres_data/9ps4_71822/02_2026/9ps4_71822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ps4_71822/02_2026/9ps4_71822.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 54 5.16 5 C 7572 2.51 5 N 1824 2.21 5 O 1923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11373 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3791 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 21, 'TRANS': 468} Chain breaks: 1 Chain: "B" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3791 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 21, 'TRANS': 468} Chain breaks: 1 Chain: "C" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3791 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 21, 'TRANS': 468} Chain breaks: 1 Time building chain proxies: 2.86, per 1000 atoms: 0.25 Number of scatterers: 11373 At special positions: 0 Unit cell: (127.28, 126.42, 80.84, 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 54 16.00 O 1923 8.00 N 1824 7.00 C 7572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 89 " distance=1.47 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 74 " distance=2.02 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 74 " distance=1.49 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 638.5 milliseconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 9 sheets defined 83.7% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 54 through 59 removed outlier: 4.164A pdb=" N SER A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 95 through 121 removed outlier: 3.524A pdb=" N ALA A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 136 through 162 removed outlier: 4.357A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 193 removed outlier: 3.547A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 223 Processing helix chain 'A' and resid 227 through 256 removed outlier: 3.606A pdb=" N GLN A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 253 " --> pdb=" O TRP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 313 through 320 removed outlier: 3.911A pdb=" N THR A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 342 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 355 through 374 removed outlier: 3.763A pdb=" N VAL A 364 " --> pdb=" O CYS A 360 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 390 through 409 Processing helix chain 'A' and resid 417 through 451 removed outlier: 3.980A pdb=" N PHE A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 423 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 436 " --> pdb=" O TRP A 432 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 482 removed outlier: 3.911A pdb=" N LEU A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASP A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 515 removed outlier: 3.572A pdb=" N ALA A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 549 Proline residue: A 547 - end of helix Processing helix chain 'A' and resid 554 through 577 removed outlier: 4.161A pdb=" N GLY A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 removed outlier: 4.164A pdb=" N SER B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 63 through 70 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 95 through 121 removed outlier: 3.649A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 136 through 162 removed outlier: 4.356A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Proline residue: B 152 - end of helix Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 193 removed outlier: 3.547A pdb=" N VAL B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 223 Processing helix chain 'B' and resid 227 through 256 removed outlier: 3.746A pdb=" N ARG B 255 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 313 through 320 removed outlier: 3.909A pdb=" N THR B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 342 Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 355 through 374 removed outlier: 3.763A pdb=" N VAL B 364 " --> pdb=" O CYS B 360 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 390 through 409 Processing helix chain 'B' and resid 417 through 451 removed outlier: 3.980A pdb=" N PHE B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 422 " --> pdb=" O HIS B 418 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 423 " --> pdb=" O TRP B 419 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 429 " --> pdb=" O GLY B 425 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA B 436 " --> pdb=" O TRP B 432 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 446 " --> pdb=" O ASN B 442 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 461 through 482 removed outlier: 4.892A pdb=" N GLY B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 515 removed outlier: 3.573A pdb=" N ALA B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE B 492 " --> pdb=" O PHE B 488 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 549 Proline residue: B 547 - end of helix Processing helix chain 'B' and resid 554 through 577 removed outlier: 4.162A pdb=" N GLY B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 59 removed outlier: 4.163A pdb=" N SER C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 62 No H-bonds generated for 'chain 'C' and resid 60 through 62' Processing helix chain 'C' and resid 63 through 70 Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 121 removed outlier: 3.640A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 Processing helix chain 'C' and resid 136 through 162 removed outlier: 4.357A pdb=" N LEU C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 166 through 193 removed outlier: 3.547A pdb=" N VAL C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 223 Processing helix chain 'C' and resid 227 through 256 removed outlier: 3.510A pdb=" N GLN C 252 " --> pdb=" O THR C 248 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 Processing helix chain 'C' and resid 313 through 320 removed outlier: 3.910A pdb=" N THR C 319 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 342 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 355 through 372 removed outlier: 3.763A pdb=" N VAL C 364 " --> pdb=" O CYS C 360 " (cutoff:3.500A) Proline residue: C 367 - end of helix Processing helix chain 'C' and resid 373 through 378 removed outlier: 3.613A pdb=" N GLY C 377 " --> pdb=" O LEU C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 409 Processing helix chain 'C' and resid 417 through 451 removed outlier: 3.980A pdb=" N PHE C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 422 " --> pdb=" O HIS C 418 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 423 " --> pdb=" O TRP C 419 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER C 429 " --> pdb=" O GLY C 425 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA C 436 " --> pdb=" O TRP C 432 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER C 446 " --> pdb=" O ASN C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 482 removed outlier: 4.171A pdb=" N LEU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 515 removed outlier: 3.572A pdb=" N ALA C 487 " --> pdb=" O TYR C 483 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE C 492 " --> pdb=" O PHE C 488 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE C 495 " --> pdb=" O CYS C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 549 Proline residue: C 547 - end of helix Processing helix chain 'C' and resid 554 through 577 removed outlier: 4.161A pdb=" N GLY C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 removed outlier: 3.580A pdb=" N PHE A 195 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 384 removed outlier: 3.673A pdb=" N LEU A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 195 through 196 removed outlier: 3.581A pdb=" N PHE B 195 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AA6, first strand: chain 'B' and resid 383 through 384 removed outlier: 3.673A pdb=" N LEU B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 195 through 196 removed outlier: 3.581A pdb=" N PHE C 195 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AA9, first strand: chain 'C' and resid 383 through 384 851 hydrogen bonds defined for protein. 2541 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: 1.85 Time building geometry restraints manager: 1.26 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: 3028 1.34 - 1.46: 2145 1.46 - 1.58: 6422 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 11661 Sorted by residual: bond pdb=" CA VAL C 457 " pdb=" CB VAL C 457 " ideal model delta sigma weight residual 1.545 1.499 0.046 1.05e-02 9.07e+03 1.91e+01 bond pdb=" CA GLY A 79 " pdb=" C GLY A 79 " ideal model delta sigma weight residual 1.519 1.480 0.039 1.15e-02 7.56e+03 1.16e+01 bond pdb=" N TYR A 251 " pdb=" CA TYR A 251 " ideal model delta sigma weight residual 1.459 1.500 -0.040 1.23e-02 6.61e+03 1.08e+01 bond pdb=" N PHE A 88 " pdb=" CA PHE A 88 " ideal model delta sigma weight residual 1.457 1.419 0.038 1.29e-02 6.01e+03 8.85e+00 bond pdb=" CA SER A 446 " pdb=" C SER A 446 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.34e-02 5.57e+03 8.78e+00 ... (remaining 11656 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 15653 2.57 - 5.14: 246 5.14 - 7.72: 28 7.72 - 10.29: 5 10.29 - 12.86: 4 Bond angle restraints: 15936 Sorted by residual: angle pdb=" N GLU A 77 " pdb=" CA GLU A 77 " pdb=" C GLU A 77 " ideal model delta sigma weight residual 111.28 124.14 -12.86 1.09e+00 8.42e-01 1.39e+02 angle pdb=" N CYS A 89 " pdb=" CA CYS A 89 " pdb=" C CYS A 89 " ideal model delta sigma weight residual 111.07 123.47 -12.40 1.07e+00 8.73e-01 1.34e+02 angle pdb=" N GLY A 78 " pdb=" CA GLY A 78 " pdb=" C GLY A 78 " ideal model delta sigma weight residual 112.73 124.39 -11.66 1.20e+00 6.94e-01 9.45e+01 angle pdb=" N TYR A 379 " pdb=" CA TYR A 379 " pdb=" C TYR A 379 " ideal model delta sigma weight residual 112.38 101.95 10.43 1.22e+00 6.72e-01 7.31e+01 angle pdb=" N TYR C 379 " pdb=" CA TYR C 379 " pdb=" C TYR C 379 " ideal model delta sigma weight residual 113.20 103.90 9.30 1.21e+00 6.83e-01 5.91e+01 ... (remaining 15931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 6056 16.23 - 32.46: 485 32.46 - 48.69: 147 48.69 - 64.92: 35 64.92 - 81.15: 6 Dihedral angle restraints: 6729 sinusoidal: 2496 harmonic: 4233 Sorted by residual: dihedral pdb=" CB CYS A 53 " pdb=" SG CYS A 53 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 136.01 -43.01 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" CB CYS A 65 " pdb=" SG CYS A 65 " pdb=" SG CYS A 89 " pdb=" CB CYS A 89 " ideal model delta sinusoidal sigma weight residual 93.00 128.81 -35.81 1 1.00e+01 1.00e-02 1.81e+01 dihedral pdb=" CB CYS C 53 " pdb=" SG CYS C 53 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 61.98 31.02 1 1.00e+01 1.00e-02 1.37e+01 ... (remaining 6726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1358 0.035 - 0.070: 421 0.070 - 0.105: 126 0.105 - 0.139: 30 0.139 - 0.174: 3 Chirality restraints: 1938 Sorted by residual: chirality pdb=" CA GLU A 77 " pdb=" N GLU A 77 " pdb=" C GLU A 77 " pdb=" CB GLU A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA VAL A 457 " pdb=" N VAL A 457 " pdb=" C VAL A 457 " pdb=" CB VAL A 457 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CA CYS A 89 " pdb=" N CYS A 89 " pdb=" C CYS A 89 " pdb=" CB CYS A 89 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 1935 not shown) Planarity restraints: 1938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 69 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.46e+01 pdb=" C LYS C 69 " -0.066 2.00e-02 2.50e+03 pdb=" O LYS C 69 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG C 70 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 69 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C LYS B 69 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS B 69 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG B 70 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 252 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C GLN B 252 " 0.049 2.00e-02 2.50e+03 pdb=" O GLN B 252 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG B 253 " -0.017 2.00e-02 2.50e+03 ... (remaining 1935 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1666 2.75 - 3.29: 11804 3.29 - 3.83: 18829 3.83 - 4.36: 19864 4.36 - 4.90: 35251 Nonbonded interactions: 87414 Sorted by model distance: nonbonded pdb=" O LEU A 98 " pdb=" OG1 THR A 101 " model vdw 2.217 3.040 nonbonded pdb=" ND2 ASN B 71 " pdb=" O PRO B 72 " model vdw 2.254 3.120 nonbonded pdb=" OG SER A 554 " pdb=" N LYS A 555 " model vdw 2.311 3.120 nonbonded pdb=" OG SER B 554 " pdb=" N LYS B 555 " model vdw 2.312 3.120 nonbonded pdb=" OG SER C 554 " pdb=" N LYS C 555 " model vdw 2.313 3.120 ... (remaining 87409 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic 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: 2.080 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.090 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 0.563 11667 Z= 0.446 Angle : 0.866 33.013 15948 Z= 0.520 Chirality : 0.039 0.174 1938 Planarity : 0.005 0.058 1938 Dihedral : 13.673 81.146 3993 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.97 % Allowed : 11.89 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.22), residues: 1458 helix: 1.55 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : -0.39 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 480 TYR 0.011 0.001 TYR A 557 PHE 0.012 0.001 PHE B 497 TRP 0.015 0.001 TRP C 317 HIS 0.002 0.000 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00378 (11661) covalent geometry : angle 0.75361 (15936) SS BOND : bond 0.31937 ( 6) SS BOND : angle 15.58100 ( 12) hydrogen bonds : bond 0.14255 ( 851) hydrogen bonds : angle 5.97632 ( 2541) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 284 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 TYR cc_start: 0.7582 (t80) cc_final: 0.7295 (t80) REVERT: A 129 ILE cc_start: 0.8489 (mt) cc_final: 0.8198 (tt) REVERT: A 132 SER cc_start: 0.8215 (t) cc_final: 0.7905 (m) REVERT: A 134 LYS cc_start: 0.8357 (mttp) cc_final: 0.8052 (mttp) REVERT: A 142 VAL cc_start: 0.7410 (t) cc_final: 0.7200 (t) REVERT: A 205 ASP cc_start: 0.8382 (m-30) cc_final: 0.8164 (m-30) REVERT: A 218 THR cc_start: 0.8095 (m) cc_final: 0.7872 (m) REVERT: A 224 ARG cc_start: 0.7792 (ptm-80) cc_final: 0.7081 (ptm-80) REVERT: A 249 TRP cc_start: 0.8478 (t60) cc_final: 0.8129 (t60) REVERT: A 253 ARG cc_start: 0.7795 (ttp80) cc_final: 0.7543 (ttp80) REVERT: A 254 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7806 (tp-100) REVERT: A 458 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6741 (mt) REVERT: A 480 ARG cc_start: 0.7642 (mmm-85) cc_final: 0.7275 (mtm-85) REVERT: A 509 LEU cc_start: 0.8251 (mt) cc_final: 0.8044 (mp) REVERT: B 129 ILE cc_start: 0.8516 (mt) cc_final: 0.8267 (tt) REVERT: B 142 VAL cc_start: 0.7133 (t) cc_final: 0.6864 (t) REVERT: B 193 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8380 (mmm-85) REVERT: B 205 ASP cc_start: 0.8567 (m-30) cc_final: 0.8272 (m-30) REVERT: B 218 THR cc_start: 0.7970 (m) cc_final: 0.7761 (m) REVERT: B 225 ILE cc_start: 0.8153 (mt) cc_final: 0.7736 (pt) REVERT: B 331 LYS cc_start: 0.7375 (mtpt) cc_final: 0.7106 (ttmm) REVERT: B 353 ASN cc_start: 0.8525 (t0) cc_final: 0.8013 (t0) REVERT: C 129 ILE cc_start: 0.8551 (mt) cc_final: 0.8265 (tt) REVERT: C 132 SER cc_start: 0.8310 (t) cc_final: 0.8072 (p) REVERT: C 134 LYS cc_start: 0.8071 (mttp) cc_final: 0.7770 (mttp) REVERT: C 224 ARG cc_start: 0.7834 (ptm-80) cc_final: 0.7403 (ptm-80) REVERT: C 249 TRP cc_start: 0.8557 (t60) cc_final: 0.8042 (t60) REVERT: C 352 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7563 (mtt-85) REVERT: C 353 ASN cc_start: 0.8343 (t0) cc_final: 0.7968 (t0) REVERT: C 423 PHE cc_start: 0.8153 (m-80) cc_final: 0.7949 (m-80) REVERT: C 467 ASN cc_start: 0.8079 (m-40) cc_final: 0.7773 (m110) REVERT: C 481 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8280 (mt0) REVERT: C 496 ILE cc_start: 0.7640 (mt) cc_final: 0.7401 (tt) REVERT: C 518 GLU cc_start: 0.7498 (pt0) cc_final: 0.6623 (pt0) outliers start: 12 outliers final: 5 residues processed: 296 average time/residue: 0.1163 time to fit residues: 48.0919 Evaluate side-chains 253 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 247 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 452 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 10.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 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 252 GLN A 254 GLN B 71 ASN B 359 ASN B 455 ASN C 149 ASN C 359 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.144309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111737 restraints weight = 17427.869| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.23 r_work: 0.3257 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11667 Z= 0.183 Angle : 0.598 8.041 15948 Z= 0.302 Chirality : 0.041 0.179 1938 Planarity : 0.004 0.031 1938 Dihedral : 4.799 59.646 1587 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.27 % Allowed : 15.53 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.22), residues: 1458 helix: 2.39 (0.15), residues: 1113 sheet: None (None), residues: 0 loop : -0.14 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 204 TYR 0.018 0.002 TYR C 557 PHE 0.019 0.001 PHE B 147 TRP 0.015 0.002 TRP C 249 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00404 (11661) covalent geometry : angle 0.59726 (15936) SS BOND : bond 0.00681 ( 6) SS BOND : angle 1.00389 ( 12) hydrogen bonds : bond 0.06087 ( 851) hydrogen bonds : angle 4.04639 ( 2541) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8579 (mttp) cc_final: 0.8374 (mttp) REVERT: A 142 VAL cc_start: 0.7789 (t) cc_final: 0.7550 (t) REVERT: A 205 ASP cc_start: 0.8528 (m-30) cc_final: 0.8233 (m-30) REVERT: A 224 ARG cc_start: 0.8276 (ptm-80) cc_final: 0.7747 (ptm-80) REVERT: A 429 SER cc_start: 0.8465 (t) cc_final: 0.8200 (p) REVERT: A 431 LEU cc_start: 0.8647 (mt) cc_final: 0.8360 (mm) REVERT: A 434 ASN cc_start: 0.8512 (t0) cc_final: 0.8234 (t0) REVERT: A 467 ASN cc_start: 0.8276 (m-40) cc_final: 0.7900 (m110) REVERT: A 480 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.7759 (mtm-85) REVERT: A 509 LEU cc_start: 0.8768 (mt) cc_final: 0.8502 (mp) REVERT: B 142 VAL cc_start: 0.7529 (t) cc_final: 0.7264 (t) REVERT: B 193 ARG cc_start: 0.8514 (tpp80) cc_final: 0.8274 (tpt-90) REVERT: B 205 ASP cc_start: 0.8609 (m-30) cc_final: 0.8336 (m-30) REVERT: B 248 THR cc_start: 0.8363 (m) cc_final: 0.7279 (p) REVERT: B 253 ARG cc_start: 0.7808 (mtm110) cc_final: 0.7490 (mtm110) REVERT: B 331 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7913 (mtmm) REVERT: B 353 ASN cc_start: 0.8883 (t0) cc_final: 0.8638 (t0) REVERT: B 431 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8323 (mt) REVERT: B 434 ASN cc_start: 0.8576 (t0) cc_final: 0.8236 (t0) REVERT: B 511 ILE cc_start: 0.8891 (mt) cc_final: 0.8683 (mt) REVERT: B 549 GLN cc_start: 0.8550 (tt0) cc_final: 0.8350 (tt0) REVERT: C 129 ILE cc_start: 0.8712 (mt) cc_final: 0.8390 (tt) REVERT: C 134 LYS cc_start: 0.8468 (mttp) cc_final: 0.8229 (mttp) REVERT: C 204 ARG cc_start: 0.8538 (ttp-170) cc_final: 0.8312 (ttp-170) REVERT: C 209 TYR cc_start: 0.8752 (t80) cc_final: 0.8426 (t80) REVERT: C 210 MET cc_start: 0.8319 (ttm) cc_final: 0.8060 (mtm) REVERT: C 224 ARG cc_start: 0.8276 (ptm-80) cc_final: 0.7940 (ptm-80) REVERT: C 316 LYS cc_start: 0.8739 (tttt) cc_final: 0.8178 (tptt) REVERT: C 352 ARG cc_start: 0.8403 (mtt-85) cc_final: 0.8163 (mtt-85) REVERT: C 353 ASN cc_start: 0.8782 (t0) cc_final: 0.8443 (t0) REVERT: C 423 PHE cc_start: 0.8341 (m-80) cc_final: 0.8014 (m-80) REVERT: C 431 LEU cc_start: 0.8562 (tp) cc_final: 0.8300 (tt) REVERT: C 518 GLU cc_start: 0.7917 (pt0) cc_final: 0.7464 (pt0) outliers start: 28 outliers final: 12 residues processed: 274 average time/residue: 0.1179 time to fit residues: 44.2059 Evaluate side-chains 249 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 ASN ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN C 467 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107930 restraints weight = 17348.720| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.23 r_work: 0.3248 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11667 Z= 0.164 Angle : 0.544 7.689 15948 Z= 0.279 Chirality : 0.040 0.134 1938 Planarity : 0.003 0.031 1938 Dihedral : 4.050 43.666 1581 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.67 % Allowed : 15.21 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.22), residues: 1458 helix: 2.61 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : 0.03 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 54 TYR 0.015 0.001 TYR A 557 PHE 0.016 0.001 PHE C 122 TRP 0.014 0.002 TRP A 317 HIS 0.004 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00359 (11661) covalent geometry : angle 0.54400 (15936) SS BOND : bond 0.00176 ( 6) SS BOND : angle 0.46335 ( 12) hydrogen bonds : bond 0.05801 ( 851) hydrogen bonds : angle 3.81887 ( 2541) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8579 (mttp) cc_final: 0.8357 (mttp) REVERT: A 142 VAL cc_start: 0.7760 (t) cc_final: 0.7495 (t) REVERT: A 205 ASP cc_start: 0.8449 (m-30) cc_final: 0.8098 (m-30) REVERT: A 224 ARG cc_start: 0.8309 (ptm-80) cc_final: 0.7735 (ptm-80) REVERT: A 420 LEU cc_start: 0.8413 (mm) cc_final: 0.8211 (mt) REVERT: A 427 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8044 (mt) REVERT: A 431 LEU cc_start: 0.8657 (mt) cc_final: 0.8368 (mm) REVERT: A 434 ASN cc_start: 0.8527 (t0) cc_final: 0.8237 (t0) REVERT: A 467 ASN cc_start: 0.8346 (m-40) cc_final: 0.7986 (m-40) REVERT: A 480 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.7863 (mtm-85) REVERT: A 509 LEU cc_start: 0.8823 (mt) cc_final: 0.8568 (mp) REVERT: B 142 VAL cc_start: 0.7626 (t) cc_final: 0.7360 (t) REVERT: B 205 ASP cc_start: 0.8564 (m-30) cc_final: 0.8259 (m-30) REVERT: B 248 THR cc_start: 0.8392 (m) cc_final: 0.7380 (p) REVERT: B 253 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7402 (mtm110) REVERT: B 331 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7936 (mtmm) REVERT: B 434 ASN cc_start: 0.8610 (t0) cc_final: 0.8268 (t0) REVERT: B 511 ILE cc_start: 0.8970 (mt) cc_final: 0.8751 (mt) REVERT: B 549 GLN cc_start: 0.8586 (tt0) cc_final: 0.8333 (tt0) REVERT: C 129 ILE cc_start: 0.8708 (mt) cc_final: 0.8337 (tt) REVERT: C 134 LYS cc_start: 0.8503 (mttp) cc_final: 0.8271 (mttp) REVERT: C 142 VAL cc_start: 0.7831 (t) cc_final: 0.7626 (t) REVERT: C 205 ASP cc_start: 0.8463 (m-30) cc_final: 0.8169 (m-30) REVERT: C 209 TYR cc_start: 0.8724 (t80) cc_final: 0.8519 (t80) REVERT: C 210 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8095 (mtm) REVERT: C 231 LEU cc_start: 0.8188 (mm) cc_final: 0.7947 (mp) REVERT: C 245 ILE cc_start: 0.8130 (mm) cc_final: 0.7878 (mt) REVERT: C 352 ARG cc_start: 0.8445 (mtt-85) cc_final: 0.8239 (mtt-85) REVERT: C 353 ASN cc_start: 0.8769 (t0) cc_final: 0.8437 (t0) REVERT: C 423 PHE cc_start: 0.8221 (m-80) cc_final: 0.7835 (m-80) REVERT: C 431 LEU cc_start: 0.8655 (tp) cc_final: 0.8348 (tt) REVERT: C 498 ASN cc_start: 0.8062 (m-40) cc_final: 0.7823 (m-40) REVERT: C 499 ILE cc_start: 0.8621 (tp) cc_final: 0.8359 (tt) outliers start: 33 outliers final: 21 residues processed: 283 average time/residue: 0.1070 time to fit residues: 41.7754 Evaluate side-chains 280 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 257 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 443 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 51 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 0.0770 chunk 106 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN A 353 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN C 434 ASN C 467 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108215 restraints weight = 17511.231| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.24 r_work: 0.3250 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11667 Z= 0.145 Angle : 0.522 8.376 15948 Z= 0.267 Chirality : 0.039 0.133 1938 Planarity : 0.003 0.036 1938 Dihedral : 3.736 22.739 1577 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.43 % Allowed : 17.39 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.22), residues: 1458 helix: 2.65 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : 0.13 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 204 TYR 0.015 0.001 TYR A 557 PHE 0.026 0.001 PHE C 217 TRP 0.013 0.001 TRP A 317 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00309 (11661) covalent geometry : angle 0.52219 (15936) SS BOND : bond 0.00076 ( 6) SS BOND : angle 0.34087 ( 12) hydrogen bonds : bond 0.05414 ( 851) hydrogen bonds : angle 3.68220 ( 2541) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8537 (mttp) cc_final: 0.8321 (mttp) REVERT: A 142 VAL cc_start: 0.7752 (t) cc_final: 0.7496 (t) REVERT: A 205 ASP cc_start: 0.8395 (m-30) cc_final: 0.7984 (m-30) REVERT: A 224 ARG cc_start: 0.8258 (ptm-80) cc_final: 0.7717 (ptm-80) REVERT: A 427 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7927 (mm) REVERT: A 431 LEU cc_start: 0.8621 (mt) cc_final: 0.8355 (mm) REVERT: A 434 ASN cc_start: 0.8514 (t0) cc_final: 0.8219 (t0) REVERT: A 467 ASN cc_start: 0.8377 (m-40) cc_final: 0.7994 (m110) REVERT: A 480 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.7808 (mtm-85) REVERT: A 499 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8308 (tt) REVERT: A 509 LEU cc_start: 0.8849 (mt) cc_final: 0.8588 (mp) REVERT: B 142 VAL cc_start: 0.7631 (t) cc_final: 0.7351 (t) REVERT: B 205 ASP cc_start: 0.8535 (m-30) cc_final: 0.8205 (m-30) REVERT: B 353 ASN cc_start: 0.8961 (t0) cc_final: 0.8491 (t0) REVERT: B 370 LEU cc_start: 0.8442 (mp) cc_final: 0.8215 (mt) REVERT: B 434 ASN cc_start: 0.8621 (t0) cc_final: 0.8283 (t0) REVERT: C 134 LYS cc_start: 0.8485 (mttp) cc_final: 0.8252 (mttp) REVERT: C 142 VAL cc_start: 0.7913 (t) cc_final: 0.7701 (t) REVERT: C 205 ASP cc_start: 0.8414 (m-30) cc_final: 0.8081 (m-30) REVERT: C 210 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.8056 (mtm) REVERT: C 224 ARG cc_start: 0.8397 (ptm-80) cc_final: 0.7945 (ptm-80) REVERT: C 245 ILE cc_start: 0.8115 (mm) cc_final: 0.7862 (mt) REVERT: C 316 LYS cc_start: 0.8686 (tttt) cc_final: 0.8068 (tptt) REVERT: C 353 ASN cc_start: 0.8765 (t0) cc_final: 0.8432 (t0) REVERT: C 356 ARG cc_start: 0.8230 (tmm-80) cc_final: 0.7847 (ttt-90) REVERT: C 423 PHE cc_start: 0.8150 (m-80) cc_final: 0.7801 (m-10) REVERT: C 431 LEU cc_start: 0.8658 (tp) cc_final: 0.8340 (tt) REVERT: C 467 ASN cc_start: 0.8329 (m-40) cc_final: 0.8121 (m-40) REVERT: C 499 ILE cc_start: 0.8642 (tp) cc_final: 0.8350 (tt) outliers start: 30 outliers final: 18 residues processed: 277 average time/residue: 0.1165 time to fit residues: 44.2593 Evaluate side-chains 282 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 261 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 443 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.139004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106678 restraints weight = 17460.434| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.25 r_work: 0.3229 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11667 Z= 0.162 Angle : 0.527 8.932 15948 Z= 0.271 Chirality : 0.039 0.140 1938 Planarity : 0.003 0.032 1938 Dihedral : 3.702 17.515 1575 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.59 % Allowed : 18.12 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.22), residues: 1458 helix: 2.64 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : 0.06 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 352 TYR 0.015 0.001 TYR A 557 PHE 0.026 0.001 PHE C 217 TRP 0.012 0.001 TRP A 317 HIS 0.004 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00358 (11661) covalent geometry : angle 0.52701 (15936) SS BOND : bond 0.00049 ( 6) SS BOND : angle 0.27046 ( 12) hydrogen bonds : bond 0.05711 ( 851) hydrogen bonds : angle 3.70601 ( 2541) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8574 (mttp) cc_final: 0.8335 (mttp) REVERT: A 142 VAL cc_start: 0.7777 (t) cc_final: 0.7505 (t) REVERT: A 205 ASP cc_start: 0.8406 (m-30) cc_final: 0.7988 (m-30) REVERT: A 214 PHE cc_start: 0.8323 (m-10) cc_final: 0.8085 (m-10) REVERT: A 224 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.7742 (ptm-80) REVERT: A 427 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7945 (mm) REVERT: A 431 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8383 (mm) REVERT: A 434 ASN cc_start: 0.8520 (t0) cc_final: 0.8219 (t0) REVERT: A 467 ASN cc_start: 0.8412 (m-40) cc_final: 0.8009 (m110) REVERT: A 480 ARG cc_start: 0.8384 (mmm-85) cc_final: 0.7803 (mtm-85) REVERT: A 499 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8292 (tt) REVERT: A 509 LEU cc_start: 0.8849 (mt) cc_final: 0.8564 (mp) REVERT: B 142 VAL cc_start: 0.7676 (t) cc_final: 0.7400 (t) REVERT: B 205 ASP cc_start: 0.8501 (m-30) cc_final: 0.8154 (m-30) REVERT: B 353 ASN cc_start: 0.8950 (t0) cc_final: 0.8595 (t0) REVERT: B 427 LEU cc_start: 0.8151 (mt) cc_final: 0.7898 (mm) REVERT: B 434 ASN cc_start: 0.8629 (t0) cc_final: 0.8252 (t0) REVERT: C 129 ILE cc_start: 0.8755 (mt) cc_final: 0.8379 (tt) REVERT: C 134 LYS cc_start: 0.8487 (mttp) cc_final: 0.8255 (mttp) REVERT: C 205 ASP cc_start: 0.8418 (m-30) cc_final: 0.8076 (m-30) REVERT: C 209 TYR cc_start: 0.8852 (t80) cc_final: 0.8481 (t80) REVERT: C 210 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8055 (mtm) REVERT: C 215 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8648 (tt) REVERT: C 224 ARG cc_start: 0.8402 (ptm-80) cc_final: 0.7906 (ptm-80) REVERT: C 245 ILE cc_start: 0.8108 (mm) cc_final: 0.7871 (mt) REVERT: C 352 ARG cc_start: 0.8464 (mtt-85) cc_final: 0.8190 (mtt-85) REVERT: C 353 ASN cc_start: 0.8803 (t0) cc_final: 0.8460 (t0) REVERT: C 431 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8282 (tt) REVERT: C 499 ILE cc_start: 0.8621 (tp) cc_final: 0.8372 (tt) outliers start: 32 outliers final: 19 residues processed: 287 average time/residue: 0.1076 time to fit residues: 42.6954 Evaluate side-chains 297 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 443 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107644 restraints weight = 17628.231| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.27 r_work: 0.3230 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11667 Z= 0.141 Angle : 0.516 9.048 15948 Z= 0.265 Chirality : 0.038 0.125 1938 Planarity : 0.004 0.033 1938 Dihedral : 3.672 17.607 1575 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.51 % Allowed : 18.53 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.22), residues: 1458 helix: 2.67 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : 0.10 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 54 TYR 0.014 0.001 TYR A 557 PHE 0.032 0.001 PHE A 147 TRP 0.014 0.001 TRP B 249 HIS 0.003 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00299 (11661) covalent geometry : angle 0.51652 (15936) SS BOND : bond 0.00047 ( 6) SS BOND : angle 0.44024 ( 12) hydrogen bonds : bond 0.05393 ( 851) hydrogen bonds : angle 3.63829 ( 2541) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8568 (mttp) cc_final: 0.8319 (mttp) REVERT: A 142 VAL cc_start: 0.7773 (t) cc_final: 0.7525 (t) REVERT: A 205 ASP cc_start: 0.8388 (m-30) cc_final: 0.7944 (m-30) REVERT: A 214 PHE cc_start: 0.8273 (m-10) cc_final: 0.8043 (m-10) REVERT: A 427 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7896 (mm) REVERT: A 431 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8388 (mm) REVERT: A 434 ASN cc_start: 0.8509 (t0) cc_final: 0.8211 (t0) REVERT: A 467 ASN cc_start: 0.8400 (m-40) cc_final: 0.7999 (m110) REVERT: A 480 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.7782 (mtm-85) REVERT: A 499 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 509 LEU cc_start: 0.8835 (mt) cc_final: 0.8562 (mp) REVERT: B 142 VAL cc_start: 0.7636 (t) cc_final: 0.7348 (t) REVERT: B 205 ASP cc_start: 0.8513 (m-30) cc_final: 0.8087 (m-30) REVERT: B 215 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8437 (tt) REVERT: B 353 ASN cc_start: 0.8917 (t0) cc_final: 0.8587 (t0) REVERT: B 434 ASN cc_start: 0.8621 (t0) cc_final: 0.8253 (t0) REVERT: B 511 ILE cc_start: 0.8963 (mt) cc_final: 0.8728 (mm) REVERT: C 134 LYS cc_start: 0.8511 (mttp) cc_final: 0.8292 (mttp) REVERT: C 205 ASP cc_start: 0.8401 (m-30) cc_final: 0.8050 (m-30) REVERT: C 210 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8040 (mtm) REVERT: C 215 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8565 (tt) REVERT: C 224 ARG cc_start: 0.8524 (ptm-80) cc_final: 0.8003 (ptm-80) REVERT: C 352 ARG cc_start: 0.8534 (mtt-85) cc_final: 0.8249 (mtt-85) REVERT: C 353 ASN cc_start: 0.8785 (t0) cc_final: 0.8422 (t0) REVERT: C 431 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8272 (tt) REVERT: C 509 LEU cc_start: 0.8835 (mm) cc_final: 0.8562 (mp) outliers start: 31 outliers final: 17 residues processed: 277 average time/residue: 0.1095 time to fit residues: 41.5849 Evaluate side-chains 291 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 443 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 31 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.138088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106512 restraints weight = 17414.040| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.25 r_work: 0.3201 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11667 Z= 0.158 Angle : 0.520 9.214 15948 Z= 0.270 Chirality : 0.039 0.133 1938 Planarity : 0.004 0.031 1938 Dihedral : 3.670 18.100 1575 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.75 % Allowed : 18.69 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.22), residues: 1458 helix: 2.69 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : 0.11 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 54 TYR 0.018 0.001 TYR B 209 PHE 0.025 0.001 PHE C 217 TRP 0.013 0.001 TRP B 249 HIS 0.004 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00347 (11661) covalent geometry : angle 0.52025 (15936) SS BOND : bond 0.00039 ( 6) SS BOND : angle 0.35393 ( 12) hydrogen bonds : bond 0.05696 ( 851) hydrogen bonds : angle 3.66563 ( 2541) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 272 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8585 (mttp) cc_final: 0.8320 (mttp) REVERT: A 142 VAL cc_start: 0.7810 (t) cc_final: 0.7519 (t) REVERT: A 205 ASP cc_start: 0.8379 (m-30) cc_final: 0.7948 (m-30) REVERT: A 214 PHE cc_start: 0.8282 (m-10) cc_final: 0.8045 (m-10) REVERT: A 427 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7886 (mm) REVERT: A 431 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8403 (mm) REVERT: A 434 ASN cc_start: 0.8499 (t0) cc_final: 0.8192 (t0) REVERT: A 467 ASN cc_start: 0.8428 (m-40) cc_final: 0.8017 (m110) REVERT: A 480 ARG cc_start: 0.8393 (mmm-85) cc_final: 0.7786 (mtm-85) REVERT: A 499 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8213 (tt) REVERT: A 509 LEU cc_start: 0.8838 (mt) cc_final: 0.8557 (mp) REVERT: B 142 VAL cc_start: 0.7715 (t) cc_final: 0.7434 (t) REVERT: B 205 ASP cc_start: 0.8519 (m-30) cc_final: 0.8165 (m-30) REVERT: B 215 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8431 (tt) REVERT: B 353 ASN cc_start: 0.8908 (t0) cc_final: 0.8626 (t0) REVERT: B 434 ASN cc_start: 0.8617 (t0) cc_final: 0.8247 (t0) REVERT: B 511 ILE cc_start: 0.8965 (mt) cc_final: 0.8720 (mm) REVERT: C 130 SER cc_start: 0.8777 (t) cc_final: 0.8443 (p) REVERT: C 134 LYS cc_start: 0.8476 (mttp) cc_final: 0.8251 (mttp) REVERT: C 205 ASP cc_start: 0.8413 (m-30) cc_final: 0.8064 (m-30) REVERT: C 210 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8018 (mtm) REVERT: C 215 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8550 (tt) REVERT: C 224 ARG cc_start: 0.8536 (ptm-80) cc_final: 0.8001 (ptm-80) REVERT: C 245 ILE cc_start: 0.8062 (mm) cc_final: 0.7566 (mt) REVERT: C 248 THR cc_start: 0.8304 (m) cc_final: 0.7223 (p) REVERT: C 352 ARG cc_start: 0.8551 (mtt-85) cc_final: 0.8274 (mtt-85) REVERT: C 353 ASN cc_start: 0.8802 (t0) cc_final: 0.8390 (t0) REVERT: C 427 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7913 (mm) REVERT: C 431 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8333 (mm) REVERT: C 509 LEU cc_start: 0.8845 (mm) cc_final: 0.8548 (mp) outliers start: 34 outliers final: 18 residues processed: 280 average time/residue: 0.1140 time to fit residues: 43.9572 Evaluate side-chains 293 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 61 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106750 restraints weight = 17422.034| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.27 r_work: 0.3228 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11667 Z= 0.149 Angle : 0.519 9.414 15948 Z= 0.268 Chirality : 0.039 0.128 1938 Planarity : 0.004 0.032 1938 Dihedral : 3.647 17.767 1575 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.27 % Allowed : 19.42 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.22), residues: 1458 helix: 2.66 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : 0.14 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 54 TYR 0.023 0.002 TYR A 209 PHE 0.024 0.001 PHE C 147 TRP 0.013 0.001 TRP B 249 HIS 0.003 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00324 (11661) covalent geometry : angle 0.51884 (15936) SS BOND : bond 0.00052 ( 6) SS BOND : angle 0.33591 ( 12) hydrogen bonds : bond 0.05528 ( 851) hydrogen bonds : angle 3.64081 ( 2541) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8561 (mttp) cc_final: 0.8296 (mttp) REVERT: A 142 VAL cc_start: 0.7733 (t) cc_final: 0.7446 (t) REVERT: A 205 ASP cc_start: 0.8354 (m-30) cc_final: 0.7900 (m-30) REVERT: A 214 PHE cc_start: 0.8215 (m-10) cc_final: 0.7986 (m-10) REVERT: A 427 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7826 (mm) REVERT: A 431 LEU cc_start: 0.8627 (mt) cc_final: 0.8373 (mm) REVERT: A 434 ASN cc_start: 0.8463 (t0) cc_final: 0.8157 (t0) REVERT: A 467 ASN cc_start: 0.8434 (m-40) cc_final: 0.8024 (m110) REVERT: A 480 ARG cc_start: 0.8379 (mmm-85) cc_final: 0.7755 (mtm-85) REVERT: A 499 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8113 (tt) REVERT: A 509 LEU cc_start: 0.8780 (mt) cc_final: 0.8520 (mp) REVERT: B 142 VAL cc_start: 0.7652 (t) cc_final: 0.7366 (t) REVERT: B 205 ASP cc_start: 0.8495 (m-30) cc_final: 0.8139 (m-30) REVERT: B 215 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8342 (tt) REVERT: B 353 ASN cc_start: 0.8915 (t0) cc_final: 0.8655 (t0) REVERT: B 434 ASN cc_start: 0.8600 (t0) cc_final: 0.8232 (t0) REVERT: B 499 ILE cc_start: 0.7989 (mm) cc_final: 0.7662 (tt) REVERT: B 511 ILE cc_start: 0.8969 (mt) cc_final: 0.8713 (mm) REVERT: B 520 LYS cc_start: 0.8322 (mtmm) cc_final: 0.8064 (mtmm) REVERT: C 132 SER cc_start: 0.8806 (t) cc_final: 0.8473 (p) REVERT: C 134 LYS cc_start: 0.8454 (mttp) cc_final: 0.8227 (mttp) REVERT: C 205 ASP cc_start: 0.8401 (m-30) cc_final: 0.8047 (m-30) REVERT: C 209 TYR cc_start: 0.8741 (t80) cc_final: 0.8325 (t80) REVERT: C 210 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8000 (mtm) REVERT: C 215 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8503 (tt) REVERT: C 224 ARG cc_start: 0.8475 (ptm-80) cc_final: 0.7898 (ptm-80) REVERT: C 245 ILE cc_start: 0.7971 (mm) cc_final: 0.7462 (mt) REVERT: C 248 THR cc_start: 0.8273 (m) cc_final: 0.7194 (p) REVERT: C 352 ARG cc_start: 0.8552 (mtt-85) cc_final: 0.8274 (mtt-85) REVERT: C 353 ASN cc_start: 0.8780 (t0) cc_final: 0.8222 (t0) REVERT: C 356 ARG cc_start: 0.8215 (tmm-80) cc_final: 0.7823 (ttt-90) REVERT: C 427 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7842 (mm) REVERT: C 431 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8285 (mm) REVERT: C 499 ILE cc_start: 0.8470 (tp) cc_final: 0.8219 (tt) REVERT: C 509 LEU cc_start: 0.8810 (mm) cc_final: 0.8505 (mp) outliers start: 28 outliers final: 17 residues processed: 278 average time/residue: 0.1149 time to fit residues: 43.9250 Evaluate side-chains 291 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 79 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** B 498 ASN ** 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 = 0.3801 r_free = 0.3801 target = 0.137546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105917 restraints weight = 17304.939| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.24 r_work: 0.3196 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11667 Z= 0.165 Angle : 0.536 9.379 15948 Z= 0.278 Chirality : 0.039 0.131 1938 Planarity : 0.004 0.036 1938 Dihedral : 3.650 17.907 1575 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.27 % Allowed : 19.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.22), residues: 1458 helix: 2.64 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : 0.06 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 54 TYR 0.018 0.002 TYR A 209 PHE 0.027 0.001 PHE A 147 TRP 0.021 0.001 TRP B 249 HIS 0.004 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00364 (11661) covalent geometry : angle 0.53627 (15936) SS BOND : bond 0.00053 ( 6) SS BOND : angle 0.30686 ( 12) hydrogen bonds : bond 0.05864 ( 851) hydrogen bonds : angle 3.68463 ( 2541) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8586 (mttp) cc_final: 0.8326 (mttp) REVERT: A 142 VAL cc_start: 0.7857 (t) cc_final: 0.7537 (t) REVERT: A 205 ASP cc_start: 0.8395 (m-30) cc_final: 0.7955 (m-30) REVERT: A 214 PHE cc_start: 0.8321 (m-10) cc_final: 0.8105 (m-10) REVERT: A 427 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7954 (mm) REVERT: A 431 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8446 (mm) REVERT: A 434 ASN cc_start: 0.8489 (t0) cc_final: 0.8174 (t0) REVERT: A 467 ASN cc_start: 0.8447 (m-40) cc_final: 0.8025 (m110) REVERT: A 480 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.7799 (mtm-85) REVERT: A 499 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8211 (tt) REVERT: A 509 LEU cc_start: 0.8834 (mt) cc_final: 0.8555 (mp) REVERT: A 567 CYS cc_start: 0.8459 (m) cc_final: 0.8133 (m) REVERT: B 142 VAL cc_start: 0.7741 (t) cc_final: 0.7458 (t) REVERT: B 205 ASP cc_start: 0.8515 (m-30) cc_final: 0.8129 (m-30) REVERT: B 215 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8420 (tt) REVERT: B 253 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7782 (mtp85) REVERT: B 353 ASN cc_start: 0.8927 (t0) cc_final: 0.8688 (t0) REVERT: B 434 ASN cc_start: 0.8627 (t0) cc_final: 0.8251 (t0) REVERT: B 499 ILE cc_start: 0.8067 (mm) cc_final: 0.7748 (tt) REVERT: B 511 ILE cc_start: 0.9007 (mt) cc_final: 0.8743 (mm) REVERT: B 549 GLN cc_start: 0.8524 (tt0) cc_final: 0.8298 (tt0) REVERT: C 132 SER cc_start: 0.8798 (t) cc_final: 0.8492 (p) REVERT: C 134 LYS cc_start: 0.8460 (mttp) cc_final: 0.8227 (mttp) REVERT: C 205 ASP cc_start: 0.8398 (m-30) cc_final: 0.8030 (m-30) REVERT: C 210 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7968 (mtm) REVERT: C 215 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8546 (tt) REVERT: C 224 ARG cc_start: 0.8529 (ptm-80) cc_final: 0.7979 (ptm-80) REVERT: C 245 ILE cc_start: 0.8064 (mm) cc_final: 0.7567 (mt) REVERT: C 248 THR cc_start: 0.8313 (m) cc_final: 0.7234 (p) REVERT: C 352 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.8297 (mtt-85) REVERT: C 353 ASN cc_start: 0.8792 (t0) cc_final: 0.8198 (t0) REVERT: C 427 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7930 (mm) REVERT: C 431 LEU cc_start: 0.8612 (tp) cc_final: 0.8341 (mm) REVERT: C 499 ILE cc_start: 0.8557 (tp) cc_final: 0.8298 (tt) REVERT: C 509 LEU cc_start: 0.8849 (mm) cc_final: 0.8538 (mp) outliers start: 28 outliers final: 18 residues processed: 289 average time/residue: 0.1086 time to fit residues: 43.4614 Evaluate side-chains 302 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 277 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 91 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109083 restraints weight = 17425.604| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.31 r_work: 0.3199 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 0.039 11667 Z= 0.151 Angle : 0.544 9.765 15948 Z= 0.277 Chirality : 0.039 0.121 1938 Planarity : 0.004 0.037 1938 Dihedral : 3.660 18.103 1575 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.18 % Allowed : 21.04 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.22), residues: 1458 helix: 2.65 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : 0.03 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 54 TYR 0.029 0.002 TYR B 209 PHE 0.037 0.001 PHE B 147 TRP 0.018 0.001 TRP B 249 HIS 0.003 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00328 (11661) covalent geometry : angle 0.54454 (15936) SS BOND : bond 0.00056 ( 6) SS BOND : angle 0.29522 ( 12) hydrogen bonds : bond 0.05596 ( 851) hydrogen bonds : angle 3.65472 ( 2541) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8607 (mttp) cc_final: 0.8363 (mttp) REVERT: A 142 VAL cc_start: 0.7820 (t) cc_final: 0.7509 (t) REVERT: A 205 ASP cc_start: 0.8399 (m-30) cc_final: 0.7970 (m-30) REVERT: A 253 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7903 (ttp80) REVERT: A 427 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7955 (mm) REVERT: A 434 ASN cc_start: 0.8496 (t0) cc_final: 0.8177 (t0) REVERT: A 467 ASN cc_start: 0.8456 (m-40) cc_final: 0.8035 (m110) REVERT: A 480 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.7792 (mtm-85) REVERT: A 499 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8208 (tt) REVERT: A 509 LEU cc_start: 0.8847 (mt) cc_final: 0.8567 (mp) REVERT: B 142 VAL cc_start: 0.7731 (t) cc_final: 0.7439 (t) REVERT: B 147 PHE cc_start: 0.8012 (m-80) cc_final: 0.7744 (m-80) REVERT: B 205 ASP cc_start: 0.8486 (m-30) cc_final: 0.8057 (m-30) REVERT: B 215 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8422 (tt) REVERT: B 353 ASN cc_start: 0.8916 (t0) cc_final: 0.8667 (t0) REVERT: B 434 ASN cc_start: 0.8633 (t0) cc_final: 0.8260 (t0) REVERT: B 499 ILE cc_start: 0.8059 (mm) cc_final: 0.7751 (tt) REVERT: B 511 ILE cc_start: 0.9010 (mt) cc_final: 0.8729 (mm) REVERT: C 132 SER cc_start: 0.8807 (t) cc_final: 0.8505 (p) REVERT: C 134 LYS cc_start: 0.8473 (mttp) cc_final: 0.8252 (mttp) REVERT: C 205 ASP cc_start: 0.8434 (m-30) cc_final: 0.8079 (m-30) REVERT: C 215 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8579 (tt) REVERT: C 224 ARG cc_start: 0.8524 (ptm-80) cc_final: 0.7964 (ptm-80) REVERT: C 245 ILE cc_start: 0.8078 (mm) cc_final: 0.7580 (mt) REVERT: C 248 THR cc_start: 0.8293 (m) cc_final: 0.7207 (p) REVERT: C 316 LYS cc_start: 0.8668 (tttt) cc_final: 0.8099 (tptt) REVERT: C 352 ARG cc_start: 0.8582 (mtt-85) cc_final: 0.8321 (mtt-85) REVERT: C 353 ASN cc_start: 0.8787 (t0) cc_final: 0.8263 (t0) REVERT: C 356 ARG cc_start: 0.8205 (tmm-80) cc_final: 0.7819 (ttt-90) REVERT: C 427 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7938 (mm) REVERT: C 431 LEU cc_start: 0.8615 (tp) cc_final: 0.8352 (mm) REVERT: C 499 ILE cc_start: 0.8556 (tp) cc_final: 0.8290 (tt) outliers start: 27 outliers final: 18 residues processed: 281 average time/residue: 0.1115 time to fit residues: 43.1368 Evaluate side-chains 294 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 71 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 133 optimal weight: 0.3980 chunk 112 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 81 optimal weight: 0.0980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN C 434 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.144118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.111754 restraints weight = 17353.583| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.33 r_work: 0.3261 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11667 Z= 0.118 Angle : 0.525 9.821 15948 Z= 0.264 Chirality : 0.038 0.122 1938 Planarity : 0.004 0.038 1938 Dihedral : 3.605 17.992 1575 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.46 % Allowed : 21.44 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.22), residues: 1458 helix: 2.71 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : 0.02 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 54 TYR 0.020 0.001 TYR C 209 PHE 0.036 0.001 PHE B 147 TRP 0.018 0.001 TRP B 249 HIS 0.002 0.000 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00237 (11661) covalent geometry : angle 0.52500 (15936) SS BOND : bond 0.00064 ( 6) SS BOND : angle 0.27140 ( 12) hydrogen bonds : bond 0.04746 ( 851) hydrogen bonds : angle 3.53658 ( 2541) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2986.76 seconds wall clock time: 51 minutes 42.75 seconds (3102.75 seconds total)