Starting phenix.real_space_refine on Wed Mar 4 05:22:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6out_20205/03_2026/6out_20205.cif Found real_map, /net/cci-nas-00/data/ceres_data/6out_20205/03_2026/6out_20205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6out_20205/03_2026/6out_20205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6out_20205/03_2026/6out_20205.map" model { file = "/net/cci-nas-00/data/ceres_data/6out_20205/03_2026/6out_20205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6out_20205/03_2026/6out_20205.cif" } resolution = 2.6 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= 0.005 sd= 0.060 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 7203 2.51 5 N 1904 2.21 5 O 2344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11505 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3721 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 51, 'TRANS': 440} Chain: "B" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3843 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 52, 'TRANS': 458} Chain: "C" Number of atoms: 3715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3715 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 51, 'TRANS': 439} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 2.89, per 1000 atoms: 0.25 Number of scatterers: 11505 At special positions: 0 Unit cell: (97.37, 110.21, 104.86, 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 2344 8.00 N 1904 7.00 C 7203 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 572.7 milliseconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 19 sheets defined 11.6% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 86 through 89 Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.813A pdb=" N THR A 228 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 229' Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.564A pdb=" N HIS A 286 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 491 through 495 removed outlier: 3.640A pdb=" N GLN A 494 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 removed outlier: 3.707A pdb=" N THR B 41 " --> pdb=" O GLY B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 removed outlier: 3.771A pdb=" N ILE B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN B 58 " --> pdb=" O PRO B 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 58' Processing helix chain 'B' and resid 86 through 89 removed outlier: 3.518A pdb=" N LEU B 89 " --> pdb=" O GLY B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 90 through 97 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.574A pdb=" N PHE B 145 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.783A pdb=" N THR B 228 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 229 " --> pdb=" O GLN B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 229' Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.585A pdb=" N HIS B 286 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 491 through 495 removed outlier: 3.654A pdb=" N GLN B 494 " --> pdb=" O GLY B 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 43 removed outlier: 3.844A pdb=" N THR C 41 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 43 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.561A pdb=" N THR C 228 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 229 " --> pdb=" O GLN C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 229' Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.578A pdb=" N HIS C 286 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'C' and resid 491 through 495 removed outlier: 3.635A pdb=" N LEU C 495 " --> pdb=" O PRO C 492 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 70 removed outlier: 12.482A pdb=" N GLN A 62 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N THR A 208 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY A 66 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 203 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 84 removed outlier: 7.289A pdb=" N VAL A 79 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU A 186 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 81 " --> pdb=" O CYS A 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 255 removed outlier: 4.189A pdb=" N TYR A 431 " --> pdb=" O MET A 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 255 removed outlier: 4.808A pdb=" N LEU A 481 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 480 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR A 461 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU A 472 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 459 " --> pdb=" O GLU A 472 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS A 474 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 457 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA A 456 " --> pdb=" O TRP A 506 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TRP A 506 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 458 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 344 removed outlier: 4.092A pdb=" N TRP A 375 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN A 331 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU A 373 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR A 333 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLY A 371 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.040A pdb=" N ALA C 120 " --> pdb=" O PRO C 189 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS C 122 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU C 182 " --> pdb=" O ASP C 82 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP C 82 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS C 184 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 70 removed outlier: 12.625A pdb=" N GLN B 62 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N THR B 208 " --> pdb=" O PRO B 64 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY B 66 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.750A pdb=" N CYS B 184 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP B 82 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 182 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS B 122 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA B 120 " --> pdb=" O PRO B 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 254 removed outlier: 4.305A pdb=" N TYR B 431 " --> pdb=" O MET B 425 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 4.846A pdb=" N LEU B 481 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 480 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 471 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 456 " --> pdb=" O TRP B 506 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP B 506 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 458 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 341 through 344 removed outlier: 7.616A pdb=" N HIS B 329 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 374 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 61 through 70 removed outlier: 12.667A pdb=" N GLN C 62 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N THR C 208 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY C 66 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 203 " --> pdb=" O ALA C 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 171 through 172 removed outlier: 3.541A pdb=" N TRP C 103 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 250 through 254 removed outlier: 7.946A pdb=" N ILE C 250 " --> pdb=" O LYS C 424 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS C 424 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR C 431 " --> pdb=" O MET C 425 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 250 through 254 removed outlier: 7.946A pdb=" N ILE C 250 " --> pdb=" O LYS C 424 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS C 424 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU C 481 " --> pdb=" O VAL C 419 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE C 480 " --> pdb=" O TYR C 476 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TYR C 461 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU C 472 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU C 459 " --> pdb=" O GLU C 472 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS C 474 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA C 457 " --> pdb=" O LYS C 474 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 456 " --> pdb=" O VAL C 507 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 505 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N HIS C 460 " --> pdb=" O PHE C 503 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE C 503 " --> pdb=" O HIS C 460 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 462 " --> pdb=" O PHE C 501 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE C 501 " --> pdb=" O VAL C 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 341 through 343 removed outlier: 7.508A pdb=" N HIS C 329 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER C 374 " --> pdb=" O HIS C 329 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 705 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: 1.75 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3470 1.33 - 1.45: 1808 1.45 - 1.57: 6257 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 11622 Sorted by residual: bond pdb=" C ALA B 475 " pdb=" N TYR B 476 " ideal model delta sigma weight residual 1.327 1.282 0.045 1.39e-02 5.18e+03 1.03e+01 bond pdb=" C HIS A 381 " pdb=" N PRO A 382 " ideal model delta sigma weight residual 1.335 1.370 -0.034 1.30e-02 5.92e+03 7.00e+00 bond pdb=" C HIS B 381 " pdb=" N PRO B 382 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.81e+00 bond pdb=" C HIS C 381 " pdb=" N PRO C 382 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.46e+00 bond pdb=" CA ILE A 392 " pdb=" C ILE A 392 " ideal model delta sigma weight residual 1.524 1.499 0.026 1.05e-02 9.07e+03 5.98e+00 ... (remaining 11617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 15472 2.37 - 4.74: 415 4.74 - 7.11: 44 7.11 - 9.47: 12 9.47 - 11.84: 1 Bond angle restraints: 15944 Sorted by residual: angle pdb=" C ILE A 392 " pdb=" N PRO A 393 " pdb=" CA PRO A 393 " ideal model delta sigma weight residual 119.78 128.40 -8.62 1.03e+00 9.43e-01 7.01e+01 angle pdb=" N PRO A 382 " pdb=" CA PRO A 382 " pdb=" C PRO A 382 " ideal model delta sigma weight residual 113.47 122.55 -9.08 1.43e+00 4.89e-01 4.04e+01 angle pdb=" N THR B 348 " pdb=" CA THR B 348 " pdb=" C THR B 348 " ideal model delta sigma weight residual 113.16 120.82 -7.66 1.42e+00 4.96e-01 2.91e+01 angle pdb=" N GLY A 396 " pdb=" CA GLY A 396 " pdb=" C GLY A 396 " ideal model delta sigma weight residual 111.36 117.28 -5.92 1.17e+00 7.31e-01 2.56e+01 angle pdb=" N GLY B 19 " pdb=" CA GLY B 19 " pdb=" C GLY B 19 " ideal model delta sigma weight residual 115.30 121.63 -6.33 1.39e+00 5.18e-01 2.08e+01 ... (remaining 15939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6317 17.85 - 35.70: 448 35.70 - 53.55: 70 53.55 - 71.40: 8 71.40 - 89.25: 6 Dihedral angle restraints: 6849 sinusoidal: 2625 harmonic: 4224 Sorted by residual: dihedral pdb=" CA THR B 223 " pdb=" C THR B 223 " pdb=" N VAL B 224 " pdb=" CA VAL B 224 " ideal model delta harmonic sigma weight residual -180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASP B 198 " pdb=" C ASP B 198 " pdb=" N SER B 199 " pdb=" CA SER B 199 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA HIS A 329 " pdb=" C HIS A 329 " pdb=" N ILE A 330 " pdb=" CA ILE A 330 " ideal model delta harmonic sigma weight residual -180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1517 0.082 - 0.165: 249 0.165 - 0.247: 18 0.247 - 0.329: 2 0.329 - 0.412: 1 Chirality restraints: 1787 Sorted by residual: chirality pdb=" CB VAL A 220 " pdb=" CA VAL A 220 " pdb=" CG1 VAL A 220 " pdb=" CG2 VAL A 220 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA GLN B 20 " pdb=" N GLN B 20 " pdb=" C GLN B 20 " pdb=" CB GLN B 20 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA PRO A 382 " pdb=" N PRO A 382 " pdb=" C PRO A 382 " pdb=" CB PRO A 382 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1784 not shown) Planarity restraints: 2123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 63 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO A 64 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 377 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 378 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 211 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO C 212 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.034 5.00e-02 4.00e+02 ... (remaining 2120 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 215 2.66 - 3.22: 9398 3.22 - 3.78: 17367 3.78 - 4.34: 25308 4.34 - 4.90: 41012 Nonbonded interactions: 93300 Sorted by model distance: nonbonded pdb=" O GLN C 264 " pdb=" CG2 ILE C 392 " model vdw 2.099 3.460 nonbonded pdb=" O PRO A 249 " pdb=" O HOH A 601 " model vdw 2.203 3.040 nonbonded pdb=" O ASP A 478 " pdb=" O HOH A 602 " model vdw 2.207 3.040 nonbonded pdb=" OE1 GLN A 264 " pdb=" O HOH A 603 " model vdw 2.230 3.040 nonbonded pdb=" O THR B 179 " pdb=" O HOH B 601 " model vdw 2.240 3.040 ... (remaining 93295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 29 through 519) selection = (chain 'B' and resid 29 through 519) 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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.590 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:10.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.007 0.070 11622 Z= 0.286 Angle : 0.926 11.843 15944 Z= 0.532 Chirality : 0.061 0.412 1787 Planarity : 0.010 0.065 2123 Dihedral : 12.598 89.251 4149 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: -2.10 (0.18), residues: 1488 helix: -2.80 (0.42), residues: 76 sheet: 0.09 (0.24), residues: 382 loop : -2.02 (0.15), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 175 TYR 0.014 0.002 TYR A 369 PHE 0.027 0.003 PHE A 200 TRP 0.034 0.004 TRP A 328 HIS 0.009 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00656 (11622) covalent geometry : angle 0.92555 (15944) hydrogen bonds : bond 0.16932 ( 275) hydrogen bonds : angle 7.51345 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.8320 (mtt) cc_final: 0.7910 (mtp) REVERT: A 416 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8172 (mt-10) REVERT: A 440 GLU cc_start: 0.8612 (mp0) cc_final: 0.8339 (mp0) REVERT: C 227 LYS cc_start: 0.8891 (mttt) cc_final: 0.8491 (mmtt) REVERT: C 282 VAL cc_start: 0.8914 (m) cc_final: 0.8654 (t) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.5929 time to fit residues: 141.2116 Evaluate side-chains 164 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 74 ASN A 106 ASN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN A 259 ASN A 266 GLN B 58 ASN B 74 ASN B 95 HIS B 171 HIS B 355 HIS B 460 HIS B 512 GLN C 171 HIS C 173 ASN C 177 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.108626 restraints weight = 13607.533| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.02 r_work: 0.3081 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11622 Z= 0.194 Angle : 0.681 9.314 15944 Z= 0.350 Chirality : 0.050 0.160 1787 Planarity : 0.008 0.055 2123 Dihedral : 5.807 23.083 1569 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.63 % Favored : 96.30 % Rotamer: Outliers : 2.84 % Allowed : 9.16 % Favored : 87.99 % 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: -1.37 (0.19), residues: 1488 helix: -1.51 (0.54), residues: 82 sheet: 0.39 (0.25), residues: 380 loop : -1.47 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 175 TYR 0.012 0.002 TYR C 369 PHE 0.028 0.002 PHE A 200 TRP 0.029 0.002 TRP A 328 HIS 0.006 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00485 (11622) covalent geometry : angle 0.68093 (15944) hydrogen bonds : bond 0.04551 ( 275) hydrogen bonds : angle 6.15406 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.310 Fit side-chains REVERT: A 185 MET cc_start: 0.9184 (mtt) cc_final: 0.8865 (mtp) REVERT: A 386 GLN cc_start: 0.7833 (mp10) cc_final: 0.7566 (mm-40) REVERT: A 416 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8386 (mt-10) REVERT: B 99 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8648 (mtm) REVERT: B 468 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8193 (ttp-170) REVERT: C 227 LYS cc_start: 0.9216 (mttt) cc_final: 0.8725 (mtpt) REVERT: C 273 ASP cc_start: 0.8216 (m-30) cc_final: 0.7838 (m-30) REVERT: C 302 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7274 (t) outliers start: 36 outliers final: 15 residues processed: 195 average time/residue: 0.5826 time to fit residues: 122.6431 Evaluate side-chains 187 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 497 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 14 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 145 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 127 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 259 ASN B 116 ASN C 50 ASN C 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108476 restraints weight = 13721.407| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.88 r_work: 0.3094 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11622 Z= 0.165 Angle : 0.640 8.064 15944 Z= 0.326 Chirality : 0.049 0.151 1787 Planarity : 0.007 0.052 2123 Dihedral : 5.521 23.104 1569 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.16 % Allowed : 10.43 % Favored : 86.41 % 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: -1.00 (0.20), residues: 1488 helix: -1.03 (0.56), residues: 82 sheet: 0.50 (0.25), residues: 385 loop : -1.16 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 175 TYR 0.012 0.002 TYR B 343 PHE 0.024 0.002 PHE A 200 TRP 0.027 0.002 TRP A 328 HIS 0.006 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00413 (11622) covalent geometry : angle 0.63950 (15944) hydrogen bonds : bond 0.04078 ( 275) hydrogen bonds : angle 5.89760 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.504 Fit side-chains REVERT: A 185 MET cc_start: 0.9188 (mtt) cc_final: 0.8835 (mtp) REVERT: A 416 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8269 (mt-10) REVERT: B 468 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8166 (ttp-170) REVERT: C 33 MET cc_start: 0.9064 (mtp) cc_final: 0.8802 (mtp) REVERT: C 227 LYS cc_start: 0.9207 (mttt) cc_final: 0.8530 (mmtt) REVERT: C 273 ASP cc_start: 0.8173 (m-30) cc_final: 0.7750 (m-30) REVERT: C 302 THR cc_start: 0.7855 (p) cc_final: 0.7361 (t) REVERT: C 449 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7581 (mm110) outliers start: 40 outliers final: 20 residues processed: 190 average time/residue: 0.5493 time to fit residues: 113.3416 Evaluate side-chains 196 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 449 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 120 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 chunk 28 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 12 optimal weight: 5.9990 overall best weight: 2.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 116 ASN C 177 GLN C 178 GLN C 235 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110677 restraints weight = 13632.301| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.90 r_work: 0.3130 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11622 Z= 0.113 Angle : 0.567 6.230 15944 Z= 0.288 Chirality : 0.046 0.134 1787 Planarity : 0.006 0.049 2123 Dihedral : 5.150 23.081 1569 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 2.37 % Allowed : 11.77 % Favored : 85.86 % 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: -0.65 (0.20), residues: 1488 helix: -0.65 (0.58), residues: 82 sheet: 0.71 (0.25), residues: 375 loop : -0.90 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 509 TYR 0.011 0.001 TYR B 343 PHE 0.016 0.001 PHE A 200 TRP 0.022 0.002 TRP A 328 HIS 0.005 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00282 (11622) covalent geometry : angle 0.56733 (15944) hydrogen bonds : bond 0.03366 ( 275) hydrogen bonds : angle 5.62321 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.495 Fit side-chains REVERT: A 416 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8175 (mt-10) REVERT: B 295 ASN cc_start: 0.7870 (t0) cc_final: 0.7381 (p0) REVERT: B 329 HIS cc_start: 0.6661 (OUTLIER) cc_final: 0.5716 (p-80) REVERT: B 468 ARG cc_start: 0.8610 (mtm-85) cc_final: 0.8129 (ttp-170) REVERT: C 33 MET cc_start: 0.9093 (mtp) cc_final: 0.8807 (mtp) REVERT: C 181 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7881 (ptm-80) REVERT: C 227 LYS cc_start: 0.9215 (mttt) cc_final: 0.8524 (mmtt) REVERT: C 273 ASP cc_start: 0.8152 (m-30) cc_final: 0.7690 (m-30) REVERT: C 282 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8931 (t) REVERT: C 302 THR cc_start: 0.7715 (p) cc_final: 0.7405 (t) REVERT: C 449 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7447 (mm110) outliers start: 30 outliers final: 14 residues processed: 201 average time/residue: 0.5623 time to fit residues: 122.3858 Evaluate side-chains 197 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 449 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 51 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 329 HIS C 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.110708 restraints weight = 13503.058| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.07 r_work: 0.3117 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11622 Z= 0.122 Angle : 0.574 6.298 15944 Z= 0.290 Chirality : 0.047 0.153 1787 Planarity : 0.006 0.048 2123 Dihedral : 5.058 22.440 1569 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.16 % Allowed : 12.01 % Favored : 84.83 % 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: -0.48 (0.21), residues: 1488 helix: -0.46 (0.58), residues: 82 sheet: 0.74 (0.25), residues: 375 loop : -0.75 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.011 0.001 TYR C 431 PHE 0.016 0.001 PHE A 200 TRP 0.030 0.002 TRP A 375 HIS 0.004 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00304 (11622) covalent geometry : angle 0.57448 (15944) hydrogen bonds : bond 0.03400 ( 275) hydrogen bonds : angle 5.55928 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.428 Fit side-chains REVERT: A 261 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: A 329 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.6936 (p90) REVERT: A 416 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8193 (mt-10) REVERT: B 295 ASN cc_start: 0.7849 (t0) cc_final: 0.7452 (p0) REVERT: B 329 HIS cc_start: 0.6713 (OUTLIER) cc_final: 0.5793 (p-80) REVERT: C 33 MET cc_start: 0.9078 (mtp) cc_final: 0.8866 (mtp) REVERT: C 227 LYS cc_start: 0.9216 (mttt) cc_final: 0.8544 (mmtt) REVERT: C 273 ASP cc_start: 0.8142 (m-30) cc_final: 0.7679 (m-30) REVERT: C 282 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8961 (t) REVERT: C 302 THR cc_start: 0.7734 (p) cc_final: 0.7460 (t) REVERT: C 449 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7478 (mm110) REVERT: C 455 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: C 468 ARG cc_start: 0.8062 (ttm170) cc_final: 0.7816 (ttt-90) outliers start: 40 outliers final: 22 residues processed: 204 average time/residue: 0.5832 time to fit residues: 128.3410 Evaluate side-chains 191 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 455 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 116 ASN C 135 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.139748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.108778 restraints weight = 13597.155| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.77 r_work: 0.3110 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11622 Z= 0.154 Angle : 0.605 7.471 15944 Z= 0.308 Chirality : 0.048 0.163 1787 Planarity : 0.006 0.052 2123 Dihedral : 5.183 23.832 1569 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.76 % Allowed : 12.72 % Favored : 84.52 % 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: -0.49 (0.20), residues: 1488 helix: -0.53 (0.58), residues: 82 sheet: 0.76 (0.25), residues: 372 loop : -0.75 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.015 0.002 TYR B 343 PHE 0.026 0.001 PHE B 312 TRP 0.041 0.002 TRP A 375 HIS 0.011 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00386 (11622) covalent geometry : angle 0.60489 (15944) hydrogen bonds : bond 0.03760 ( 275) hydrogen bonds : angle 5.61371 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.438 Fit side-chains REVERT: A 261 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: A 416 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 295 ASN cc_start: 0.7826 (t0) cc_final: 0.7485 (p0) REVERT: B 329 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6104 (p-80) REVERT: B 468 ARG cc_start: 0.8570 (mtm180) cc_final: 0.8275 (ttp-170) REVERT: B 509 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7966 (ttm-80) REVERT: C 33 MET cc_start: 0.9054 (mtp) cc_final: 0.8815 (mtp) REVERT: C 227 LYS cc_start: 0.9205 (mttt) cc_final: 0.8549 (mmtt) REVERT: C 273 ASP cc_start: 0.8102 (m-30) cc_final: 0.7643 (m-30) REVERT: C 282 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8919 (t) REVERT: C 302 THR cc_start: 0.7731 (p) cc_final: 0.7468 (t) REVERT: C 329 HIS cc_start: 0.6094 (OUTLIER) cc_final: 0.5739 (p-80) REVERT: C 449 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7525 (mm110) REVERT: C 455 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: C 468 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7750 (ttt-90) outliers start: 35 outliers final: 20 residues processed: 186 average time/residue: 0.5275 time to fit residues: 106.6963 Evaluate side-chains 196 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 455 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 58 ASN B 116 ASN C 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.107607 restraints weight = 13726.949| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.80 r_work: 0.3093 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11622 Z= 0.174 Angle : 0.638 8.482 15944 Z= 0.324 Chirality : 0.049 0.163 1787 Planarity : 0.006 0.057 2123 Dihedral : 5.311 25.087 1569 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.92 % Allowed : 13.03 % Favored : 84.04 % 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: -0.53 (0.20), residues: 1488 helix: -0.57 (0.57), residues: 82 sheet: 0.61 (0.25), residues: 385 loop : -0.74 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 175 TYR 0.014 0.002 TYR B 343 PHE 0.028 0.002 PHE B 312 TRP 0.032 0.002 TRP A 375 HIS 0.004 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00437 (11622) covalent geometry : angle 0.63817 (15944) hydrogen bonds : bond 0.03978 ( 275) hydrogen bonds : angle 5.70326 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.473 Fit side-chains REVERT: A 261 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: A 416 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8292 (mt-10) REVERT: B 295 ASN cc_start: 0.7855 (t0) cc_final: 0.7477 (p0) REVERT: B 329 HIS cc_start: 0.7126 (OUTLIER) cc_final: 0.6179 (p-80) REVERT: B 468 ARG cc_start: 0.8583 (mtm180) cc_final: 0.8374 (mtp180) REVERT: B 509 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7974 (ttm-80) REVERT: C 33 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8802 (mtp) REVERT: C 227 LYS cc_start: 0.9212 (mttt) cc_final: 0.8537 (mmtt) REVERT: C 273 ASP cc_start: 0.8107 (m-30) cc_final: 0.7654 (m-30) REVERT: C 302 THR cc_start: 0.7480 (p) cc_final: 0.7242 (t) REVERT: C 449 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7528 (mm110) REVERT: C 455 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: C 468 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7735 (ttt-90) outliers start: 37 outliers final: 23 residues processed: 190 average time/residue: 0.5475 time to fit residues: 112.6410 Evaluate side-chains 194 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 33 MET Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 455 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 94 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 49 optimal weight: 0.0370 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 116 ASN C 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.142484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.112416 restraints weight = 13598.815| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.01 r_work: 0.3145 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11622 Z= 0.096 Angle : 0.535 6.010 15944 Z= 0.272 Chirality : 0.046 0.152 1787 Planarity : 0.006 0.062 2123 Dihedral : 4.849 22.442 1569 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.37 % Allowed : 13.67 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.24 (0.21), residues: 1488 helix: -0.12 (0.62), residues: 77 sheet: 0.78 (0.26), residues: 376 loop : -0.52 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.009 0.001 TYR C 431 PHE 0.029 0.001 PHE B 312 TRP 0.018 0.002 TRP A 328 HIS 0.003 0.000 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00237 (11622) covalent geometry : angle 0.53490 (15944) hydrogen bonds : bond 0.02950 ( 275) hydrogen bonds : angle 5.37825 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.454 Fit side-chains REVERT: A 416 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 295 ASN cc_start: 0.7712 (t0) cc_final: 0.7444 (p0) REVERT: B 313 GLU cc_start: 0.7682 (pm20) cc_final: 0.7414 (pm20) REVERT: B 329 HIS cc_start: 0.6924 (OUTLIER) cc_final: 0.6024 (p-80) REVERT: B 468 ARG cc_start: 0.8549 (mtm180) cc_final: 0.8337 (mtp180) REVERT: C 33 MET cc_start: 0.9086 (mtp) cc_final: 0.8843 (mtp) REVERT: C 181 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7744 (ptm-80) REVERT: C 227 LYS cc_start: 0.9204 (mttt) cc_final: 0.8506 (mmtt) REVERT: C 273 ASP cc_start: 0.8138 (m-30) cc_final: 0.7663 (m-30) REVERT: C 282 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8946 (t) REVERT: C 329 HIS cc_start: 0.5906 (OUTLIER) cc_final: 0.5499 (p-80) REVERT: C 468 ARG cc_start: 0.7971 (ttm170) cc_final: 0.7726 (ttt-90) outliers start: 30 outliers final: 16 residues processed: 188 average time/residue: 0.5673 time to fit residues: 115.4538 Evaluate side-chains 179 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 329 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 79 optimal weight: 10.0000 chunk 21 optimal weight: 0.2980 chunk 46 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 36 optimal weight: 0.0570 chunk 5 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 overall best weight: 3.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 259 ASN A 355 HIS B 116 ASN C 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110339 restraints weight = 13497.910| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.78 r_work: 0.3132 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11622 Z= 0.118 Angle : 0.567 6.425 15944 Z= 0.288 Chirality : 0.047 0.159 1787 Planarity : 0.006 0.062 2123 Dihedral : 4.869 22.904 1569 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.58 % Allowed : 14.77 % Favored : 83.65 % 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: -0.18 (0.21), residues: 1488 helix: -0.00 (0.62), residues: 76 sheet: 0.77 (0.25), residues: 376 loop : -0.47 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.014 0.001 TYR C 431 PHE 0.029 0.001 PHE B 312 TRP 0.018 0.002 TRP A 328 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00296 (11622) covalent geometry : angle 0.56710 (15944) hydrogen bonds : bond 0.03291 ( 275) hydrogen bonds : angle 5.42023 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.448 Fit side-chains REVERT: B 468 ARG cc_start: 0.8554 (mtm180) cc_final: 0.8350 (mtp180) REVERT: C 33 MET cc_start: 0.9068 (mtp) cc_final: 0.8789 (mtp) REVERT: C 163 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8213 (mp0) REVERT: C 227 LYS cc_start: 0.9163 (mttt) cc_final: 0.8508 (mmtt) REVERT: C 273 ASP cc_start: 0.8123 (m-30) cc_final: 0.7620 (m-30) REVERT: C 329 HIS cc_start: 0.6135 (OUTLIER) cc_final: 0.5749 (p-80) REVERT: C 373 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8682 (tm) REVERT: C 437 LEU cc_start: 0.8290 (mt) cc_final: 0.8084 (mt) outliers start: 20 outliers final: 15 residues processed: 176 average time/residue: 0.5842 time to fit residues: 111.1032 Evaluate side-chains 177 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 123 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 259 ASN B 116 ASN C 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107943 restraints weight = 13811.450| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.04 r_work: 0.3073 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11622 Z= 0.192 Angle : 0.660 9.170 15944 Z= 0.338 Chirality : 0.050 0.159 1787 Planarity : 0.006 0.062 2123 Dihedral : 5.273 25.726 1569 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.82 % Allowed : 14.85 % Favored : 83.33 % 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: -0.36 (0.21), residues: 1488 helix: -0.18 (0.61), residues: 76 sheet: 0.62 (0.25), residues: 385 loop : -0.59 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 509 TYR 0.020 0.002 TYR C 431 PHE 0.033 0.002 PHE B 312 TRP 0.018 0.002 TRP B 328 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00484 (11622) covalent geometry : angle 0.66027 (15944) hydrogen bonds : bond 0.04090 ( 275) hydrogen bonds : angle 5.68714 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.462 Fit side-chains REVERT: A 416 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8305 (mt-10) REVERT: B 329 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6128 (p-80) REVERT: B 468 ARG cc_start: 0.8591 (mtm180) cc_final: 0.8390 (mtp180) REVERT: C 33 MET cc_start: 0.9082 (mtp) cc_final: 0.8866 (mtp) REVERT: C 163 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8302 (mp0) REVERT: C 227 LYS cc_start: 0.9199 (mttt) cc_final: 0.8520 (mmtt) REVERT: C 273 ASP cc_start: 0.8144 (m-30) cc_final: 0.7673 (m-30) REVERT: C 373 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8747 (tm) REVERT: C 455 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7827 (tt0) outliers start: 23 outliers final: 16 residues processed: 177 average time/residue: 0.5703 time to fit residues: 109.3108 Evaluate side-chains 176 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 455 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 0.4980 chunk 89 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 259 ASN B 116 ASN B 460 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.112665 restraints weight = 13676.355| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.03 r_work: 0.3153 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11622 Z= 0.097 Angle : 0.544 6.599 15944 Z= 0.276 Chirality : 0.046 0.176 1787 Planarity : 0.006 0.067 2123 Dihedral : 4.777 22.007 1569 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.50 % Allowed : 15.09 % Favored : 83.41 % 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: -0.10 (0.21), residues: 1488 helix: -0.02 (0.62), residues: 77 sheet: 0.78 (0.25), residues: 376 loop : -0.38 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.014 0.001 TYR C 431 PHE 0.032 0.001 PHE B 312 TRP 0.020 0.002 TRP A 375 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00241 (11622) covalent geometry : angle 0.54375 (15944) hydrogen bonds : bond 0.02872 ( 275) hydrogen bonds : angle 5.32552 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4108.51 seconds wall clock time: 70 minutes 30.46 seconds (4230.46 seconds total)