Starting phenix.real_space_refine on Sun Apr 5 17:42:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e7i_47676/04_2026/9e7i_47676.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e7i_47676/04_2026/9e7i_47676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e7i_47676/04_2026/9e7i_47676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e7i_47676/04_2026/9e7i_47676.map" model { file = "/net/cci-nas-00/data/ceres_data/9e7i_47676/04_2026/9e7i_47676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e7i_47676/04_2026/9e7i_47676.cif" } resolution = 2.5 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= 0.052 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 60 5.16 5 C 7467 2.51 5 N 2058 2.21 5 O 2247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11832 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3916 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 463} Chain breaks: 5 Chain: "B" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3916 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 463} Chain breaks: 5 Chain: "C" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3916 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 463} Chain breaks: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.66, per 1000 atoms: 0.22 Number of scatterers: 11832 At special positions: 0 Unit cell: (123.42, 125.4, 95.7, 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 60 16.00 O 2247 8.00 N 2058 7.00 C 7467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.04 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.04 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 141 " " NAG A1002 " - " ASN A 430 " " NAG B1001 " - " ASN B 141 " " NAG B1002 " - " ASN B 430 " " NAG C1001 " - " ASN C 141 " " NAG C1002 " - " ASN C 430 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 469.1 milliseconds 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 24 sheets defined 21.5% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.912A pdb=" N THR A 309 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 413 through 429 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.866A pdb=" N HIS A 516 " --> pdb=" O HIS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 544 removed outlier: 3.740A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.900A pdb=" N THR B 309 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.530A pdb=" N ARG B 406 " --> pdb=" O PRO B 403 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 407 " --> pdb=" O LEU B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 407' Processing helix chain 'B' and resid 413 through 429 Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 510 through 531 removed outlier: 3.936A pdb=" N HIS B 516 " --> pdb=" O HIS B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 544 removed outlier: 3.769A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.889A pdb=" N THR C 309 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.566A pdb=" N ARG C 406 " --> pdb=" O PRO C 403 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 407 " --> pdb=" O LEU C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 407' Processing helix chain 'C' and resid 413 through 429 Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 510 through 531 removed outlier: 3.875A pdb=" N HIS C 516 " --> pdb=" O HIS C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 544 removed outlier: 3.727A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.160A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA3, first strand: chain 'A' and resid 433 through 435 removed outlier: 6.257A pdb=" N LEU A 443 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN A 398 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU A 374 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY A 145 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A 376 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR A 143 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER A 378 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN A 141 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 13.937A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 191 Processing sheet with id=AA5, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.121A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N THR A 340 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 324 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA7, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AA8, first strand: chain 'A' and resid 638 through 642 removed outlier: 3.780A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.192A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB2, first strand: chain 'B' and resid 433 through 435 removed outlier: 6.250A pdb=" N LEU B 443 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN B 398 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU B 374 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY B 145 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 376 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 143 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER B 378 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASN B 141 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 13.956A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 189 through 191 Processing sheet with id=AB4, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.109A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 324 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 206 through 207 Processing sheet with id=AB6, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AB7, first strand: chain 'B' and resid 638 through 642 removed outlier: 3.782A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.179A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 124 through 125 Processing sheet with id=AC1, first strand: chain 'C' and resid 433 through 435 removed outlier: 6.252A pdb=" N LEU C 443 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN C 398 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU C 374 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY C 145 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C 376 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR C 143 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER C 378 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN C 141 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 13.957A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 189 through 191 Processing sheet with id=AC3, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.092A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AC5, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AC6, first strand: chain 'C' and resid 638 through 642 removed outlier: 3.766A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1335 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: 1.86 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1943 1.32 - 1.44: 3540 1.44 - 1.57: 6547 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 12120 Sorted by residual: bond pdb=" N VAL A 281 " pdb=" CA VAL A 281 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.27e+01 bond pdb=" N VAL B 281 " pdb=" CA VAL B 281 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.15e-02 7.56e+03 1.16e+01 bond pdb=" N VAL C 281 " pdb=" CA VAL C 281 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.16e+01 bond pdb=" C PHE C 287 " pdb=" O PHE C 287 " ideal model delta sigma weight residual 1.234 1.195 0.039 1.24e-02 6.50e+03 9.77e+00 bond pdb=" C PHE A 287 " pdb=" O PHE A 287 " ideal model delta sigma weight residual 1.234 1.197 0.036 1.24e-02 6.50e+03 8.51e+00 ... (remaining 12115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 16026 1.77 - 3.55: 362 3.55 - 5.32: 59 5.32 - 7.09: 9 7.09 - 8.86: 8 Bond angle restraints: 16464 Sorted by residual: angle pdb=" CA PHE C 287 " pdb=" CB PHE C 287 " pdb=" CG PHE C 287 " ideal model delta sigma weight residual 113.80 122.06 -8.26 1.00e+00 1.00e+00 6.83e+01 angle pdb=" CA PHE A 287 " pdb=" CB PHE A 287 " pdb=" CG PHE A 287 " ideal model delta sigma weight residual 113.80 121.53 -7.73 1.00e+00 1.00e+00 5.97e+01 angle pdb=" CA PHE B 287 " pdb=" CB PHE B 287 " pdb=" CG PHE B 287 " ideal model delta sigma weight residual 113.80 119.45 -5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" N PRO B 283 " pdb=" CD PRO B 283 " pdb=" CG PRO B 283 " ideal model delta sigma weight residual 103.80 97.49 6.31 1.20e+00 6.94e-01 2.76e+01 angle pdb=" N PRO C 283 " pdb=" CD PRO C 283 " pdb=" CG PRO C 283 " ideal model delta sigma weight residual 103.80 97.54 6.26 1.20e+00 6.94e-01 2.72e+01 ... (remaining 16459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 6200 16.16 - 32.32: 721 32.32 - 48.47: 249 48.47 - 64.63: 84 64.63 - 80.79: 24 Dihedral angle restraints: 7278 sinusoidal: 2976 harmonic: 4302 Sorted by residual: dihedral pdb=" CA TYR A 282 " pdb=" C TYR A 282 " pdb=" N PRO A 283 " pdb=" CA PRO A 283 " ideal model delta harmonic sigma weight residual 0.00 24.71 -24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ARG B 427 " pdb=" C ARG B 427 " pdb=" N ARG B 428 " pdb=" CA ARG B 428 " ideal model delta harmonic sigma weight residual -180.00 -162.51 -17.49 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA THR B 143 " pdb=" C THR B 143 " pdb=" N GLU B 144 " pdb=" CA GLU B 144 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 7275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1348 0.047 - 0.094: 347 0.094 - 0.140: 85 0.140 - 0.187: 13 0.187 - 0.234: 7 Chirality restraints: 1800 Sorted by residual: chirality pdb=" C1 NAG B1002 " pdb=" ND2 ASN B 430 " pdb=" C2 NAG B1002 " pdb=" O5 NAG B1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1 NAG A1002 " pdb=" ND2 ASN A 430 " pdb=" C2 NAG A1002 " pdb=" O5 NAG A1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ASP A 285 " pdb=" N ASP A 285 " pdb=" C ASP A 285 " pdb=" CB ASP A 285 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1797 not shown) Planarity restraints: 2145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 287 " -0.029 2.00e-02 2.50e+03 1.85e-02 6.00e+00 pdb=" CG PHE C 287 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE C 287 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 287 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 287 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 287 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 287 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 278 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C ALA A 278 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA A 278 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG A 279 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 287 " -0.028 2.00e-02 2.50e+03 1.74e-02 5.33e+00 pdb=" CG PHE A 287 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 287 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 287 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 287 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 287 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 287 " -0.015 2.00e-02 2.50e+03 ... (remaining 2142 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1684 2.76 - 3.29: 9934 3.29 - 3.83: 19710 3.83 - 4.36: 24632 4.36 - 4.90: 41418 Nonbonded interactions: 97378 Sorted by model distance: nonbonded pdb=" O PHE A 503 " pdb=" NH1 ARG A 505 " model vdw 2.225 3.120 nonbonded pdb=" O PHE C 503 " pdb=" NH1 ARG C 505 " model vdw 2.270 3.120 nonbonded pdb=" O PHE B 503 " pdb=" NH1 ARG B 505 " model vdw 2.271 3.120 nonbonded pdb=" O PRO C 119 " pdb=" NH1 ARG C 562 " model vdw 2.297 3.120 nonbonded pdb=" O PRO B 119 " pdb=" NH1 ARG B 562 " model vdw 2.300 3.120 ... (remaining 97373 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: 9.270 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.390 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 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 : 0.004 0.040 12132 Z= 0.216 Angle : 0.667 8.865 16494 Z= 0.389 Chirality : 0.046 0.234 1800 Planarity : 0.005 0.057 2139 Dihedral : 17.235 80.791 4494 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 6.62 % Allowed : 17.46 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.19 (0.21), residues: 1431 helix: 1.37 (0.32), residues: 228 sheet: 1.11 (0.23), residues: 426 loop : -0.85 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.014 0.001 TYR B 282 PHE 0.031 0.002 PHE C 287 TRP 0.018 0.002 TRP A 539 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00426 (12120) covalent geometry : angle 0.66110 (16464) SS BOND : bond 0.00465 ( 6) SS BOND : angle 1.09681 ( 12) hydrogen bonds : bond 0.16361 ( 457) hydrogen bonds : angle 6.64642 ( 1335) link_NAG-ASN : bond 0.00292 ( 6) link_NAG-ASN : angle 2.55958 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 140 time to evaluate : 0.483 Fit side-chains REVERT: A 128 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7982 (mm-30) REVERT: A 401 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: A 415 LYS cc_start: 0.8266 (ttpm) cc_final: 0.7910 (tttp) REVERT: A 585 ASN cc_start: 0.7684 (m-40) cc_final: 0.7325 (m-40) REVERT: A 619 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8478 (mt-10) REVERT: B 409 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.4979 (mp) REVERT: B 415 LYS cc_start: 0.8301 (ttpm) cc_final: 0.7910 (tttp) REVERT: B 585 ASN cc_start: 0.7667 (m-40) cc_final: 0.7411 (m-40) REVERT: B 619 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: C 128 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: C 286 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8280 (pt0) REVERT: C 401 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: C 415 LYS cc_start: 0.8316 (ttpm) cc_final: 0.7956 (tttp) REVERT: C 585 ASN cc_start: 0.7623 (m-40) cc_final: 0.7331 (m-40) outliers start: 83 outliers final: 65 residues processed: 199 average time/residue: 0.5492 time to fit residues: 118.7247 Evaluate side-chains 210 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 137 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 TRP Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 539 TRP Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.0070 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.154570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.118797 restraints weight = 10888.093| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.57 r_work: 0.3130 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12132 Z= 0.215 Angle : 0.648 8.878 16494 Z= 0.352 Chirality : 0.048 0.243 1800 Planarity : 0.006 0.057 2139 Dihedral : 11.014 80.417 1900 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 6.86 % Allowed : 16.03 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.07 (0.21), residues: 1431 helix: 1.11 (0.31), residues: 240 sheet: 0.85 (0.22), residues: 456 loop : -0.85 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 505 TYR 0.017 0.002 TYR B 114 PHE 0.022 0.002 PHE C 287 TRP 0.021 0.003 TRP A 539 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00509 (12120) covalent geometry : angle 0.64200 (16464) SS BOND : bond 0.00618 ( 6) SS BOND : angle 1.39496 ( 12) hydrogen bonds : bond 0.05286 ( 457) hydrogen bonds : angle 5.29320 ( 1335) link_NAG-ASN : bond 0.00269 ( 6) link_NAG-ASN : angle 2.56374 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 144 time to evaluate : 0.493 Fit side-chains REVERT: A 107 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7070 (mm-30) REVERT: A 128 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: A 401 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: A 415 LYS cc_start: 0.8308 (ttpm) cc_final: 0.7926 (tttp) REVERT: A 585 ASN cc_start: 0.7761 (m-40) cc_final: 0.7421 (m-40) REVERT: B 415 LYS cc_start: 0.8342 (ttpm) cc_final: 0.7941 (tttp) REVERT: B 585 ASN cc_start: 0.7671 (m-40) cc_final: 0.7419 (m-40) REVERT: C 112 ASN cc_start: 0.8533 (m-40) cc_final: 0.8286 (m110) REVERT: C 128 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7978 (mm-30) REVERT: C 304 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6305 (mtm180) REVERT: C 349 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7860 (mptt) REVERT: C 401 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: C 415 LYS cc_start: 0.8351 (ttpm) cc_final: 0.7986 (tttp) REVERT: C 585 ASN cc_start: 0.7699 (m-40) cc_final: 0.7415 (m-40) REVERT: C 619 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8499 (mt-10) outliers start: 86 outliers final: 58 residues processed: 213 average time/residue: 0.5835 time to fit residues: 134.1552 Evaluate side-chains 200 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 135 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 TRP Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 539 TRP Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 35 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 58 optimal weight: 0.0570 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.158419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.122735 restraints weight = 11036.450| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.58 r_work: 0.3183 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12132 Z= 0.115 Angle : 0.523 7.119 16494 Z= 0.284 Chirality : 0.042 0.206 1800 Planarity : 0.004 0.052 2139 Dihedral : 9.140 63.844 1856 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.98 % Allowed : 17.54 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.34 (0.21), residues: 1431 helix: 1.54 (0.32), residues: 240 sheet: 1.02 (0.23), residues: 456 loop : -0.75 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 505 TYR 0.011 0.001 TYR B 114 PHE 0.016 0.001 PHE C 287 TRP 0.015 0.002 TRP A 539 HIS 0.003 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00257 (12120) covalent geometry : angle 0.51895 (16464) SS BOND : bond 0.00380 ( 6) SS BOND : angle 0.96978 ( 12) hydrogen bonds : bond 0.03914 ( 457) hydrogen bonds : angle 4.89344 ( 1335) link_NAG-ASN : bond 0.00308 ( 6) link_NAG-ASN : angle 2.01974 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 148 time to evaluate : 0.330 Fit side-chains REVERT: A 107 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7077 (mm-30) REVERT: A 128 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7908 (mm-30) REVERT: A 415 LYS cc_start: 0.8303 (ttpm) cc_final: 0.7978 (tttp) REVERT: A 539 TRP cc_start: 0.7787 (OUTLIER) cc_final: 0.7425 (m-10) REVERT: A 585 ASN cc_start: 0.7681 (m-40) cc_final: 0.7343 (m-40) REVERT: A 619 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8432 (mt-10) REVERT: B 415 LYS cc_start: 0.8306 (ttpm) cc_final: 0.7946 (tttp) REVERT: B 535 GLU cc_start: 0.8385 (tt0) cc_final: 0.8170 (tt0) REVERT: B 585 ASN cc_start: 0.7573 (m-40) cc_final: 0.7329 (m-40) REVERT: B 619 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8464 (mt-10) REVERT: C 107 GLU cc_start: 0.7615 (mt-10) cc_final: 0.6860 (mm-30) REVERT: C 128 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: C 286 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: C 415 LYS cc_start: 0.8274 (ttpm) cc_final: 0.7935 (tttp) REVERT: C 535 GLU cc_start: 0.8379 (tt0) cc_final: 0.8066 (tp30) REVERT: C 585 ASN cc_start: 0.7615 (m-40) cc_final: 0.7334 (m-40) REVERT: C 619 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8507 (mt-10) outliers start: 75 outliers final: 44 residues processed: 202 average time/residue: 0.5944 time to fit residues: 129.5174 Evaluate side-chains 193 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 539 TRP Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 539 TRP Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 0.0870 chunk 4 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.155210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119199 restraints weight = 10987.503| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.59 r_work: 0.3139 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12132 Z= 0.204 Angle : 0.622 8.843 16494 Z= 0.337 Chirality : 0.047 0.236 1800 Planarity : 0.005 0.053 2139 Dihedral : 8.966 66.333 1830 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 6.78 % Allowed : 15.95 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.19 (0.21), residues: 1431 helix: 1.31 (0.32), residues: 240 sheet: 0.91 (0.23), residues: 456 loop : -0.80 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 505 TYR 0.015 0.002 TYR B 114 PHE 0.021 0.002 PHE B 287 TRP 0.020 0.003 TRP A 539 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00484 (12120) covalent geometry : angle 0.61658 (16464) SS BOND : bond 0.00611 ( 6) SS BOND : angle 1.42456 ( 12) hydrogen bonds : bond 0.04874 ( 457) hydrogen bonds : angle 5.07189 ( 1335) link_NAG-ASN : bond 0.00260 ( 6) link_NAG-ASN : angle 2.39192 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 141 time to evaluate : 0.432 Fit side-chains REVERT: A 107 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7060 (mm-30) REVERT: A 128 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7950 (mm-30) REVERT: A 415 LYS cc_start: 0.8306 (ttpm) cc_final: 0.7975 (tttp) REVERT: A 585 ASN cc_start: 0.7737 (m-40) cc_final: 0.7404 (m-40) REVERT: A 619 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8463 (mt-10) REVERT: B 286 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8662 (pm20) REVERT: B 415 LYS cc_start: 0.8354 (ttpm) cc_final: 0.7960 (tttp) REVERT: B 535 GLU cc_start: 0.8496 (tt0) cc_final: 0.8288 (tt0) REVERT: B 585 ASN cc_start: 0.7643 (m-40) cc_final: 0.7394 (m-40) REVERT: B 619 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: C 235 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7548 (mptp) REVERT: C 286 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8166 (pm20) REVERT: C 304 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6472 (mtm180) REVERT: C 349 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7925 (mptt) REVERT: C 415 LYS cc_start: 0.8357 (ttpm) cc_final: 0.7995 (tttp) REVERT: C 585 ASN cc_start: 0.7664 (m-40) cc_final: 0.7380 (m-40) REVERT: C 619 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8514 (mt-10) outliers start: 85 outliers final: 60 residues processed: 205 average time/residue: 0.5765 time to fit residues: 127.8824 Evaluate side-chains 208 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 140 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 TRP Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 539 TRP Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.155548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.119656 restraints weight = 10947.772| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.58 r_work: 0.3147 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12132 Z= 0.180 Angle : 0.600 8.453 16494 Z= 0.324 Chirality : 0.046 0.228 1800 Planarity : 0.005 0.053 2139 Dihedral : 8.692 65.931 1827 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 7.66 % Allowed : 15.23 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.17 (0.21), residues: 1431 helix: 1.28 (0.31), residues: 240 sheet: 0.91 (0.23), residues: 456 loop : -0.81 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 505 TYR 0.014 0.002 TYR B 114 PHE 0.019 0.002 PHE C 287 TRP 0.019 0.002 TRP A 539 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00424 (12120) covalent geometry : angle 0.59426 (16464) SS BOND : bond 0.00561 ( 6) SS BOND : angle 1.35732 ( 12) hydrogen bonds : bond 0.04608 ( 457) hydrogen bonds : angle 5.02903 ( 1335) link_NAG-ASN : bond 0.00247 ( 6) link_NAG-ASN : angle 2.32363 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 141 time to evaluate : 0.423 Fit side-chains REVERT: A 107 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7048 (mm-30) REVERT: A 128 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8019 (mm-30) REVERT: A 286 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: A 415 LYS cc_start: 0.8283 (ttpm) cc_final: 0.7948 (tttp) REVERT: A 585 ASN cc_start: 0.7733 (m-40) cc_final: 0.7400 (m-40) REVERT: A 619 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8477 (mt-10) REVERT: B 286 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8640 (pm20) REVERT: B 379 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: B 415 LYS cc_start: 0.8362 (ttpm) cc_final: 0.7968 (tttp) REVERT: B 535 GLU cc_start: 0.8486 (tt0) cc_final: 0.8278 (tt0) REVERT: B 585 ASN cc_start: 0.7615 (m-40) cc_final: 0.7369 (m-40) REVERT: B 619 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8524 (mt-10) REVERT: C 286 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: C 304 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6552 (mtm180) REVERT: C 349 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7999 (mptt) REVERT: C 415 LYS cc_start: 0.8348 (ttpm) cc_final: 0.7988 (tttp) REVERT: C 535 GLU cc_start: 0.8450 (tt0) cc_final: 0.8154 (tp30) REVERT: C 585 ASN cc_start: 0.7657 (m-40) cc_final: 0.7371 (m-40) REVERT: C 619 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8527 (mt-10) outliers start: 96 outliers final: 65 residues processed: 211 average time/residue: 0.5910 time to fit residues: 134.6173 Evaluate side-chains 213 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 138 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 539 TRP Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 539 TRP Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.155105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119183 restraints weight = 10965.547| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.58 r_work: 0.3139 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12132 Z= 0.198 Angle : 0.621 8.757 16494 Z= 0.335 Chirality : 0.047 0.232 1800 Planarity : 0.005 0.056 2139 Dihedral : 8.804 66.091 1827 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 7.18 % Allowed : 15.79 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.11 (0.21), residues: 1431 helix: 1.19 (0.31), residues: 240 sheet: 0.89 (0.23), residues: 456 loop : -0.84 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 505 TYR 0.015 0.002 TYR B 114 PHE 0.020 0.002 PHE C 287 TRP 0.020 0.002 TRP A 539 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00470 (12120) covalent geometry : angle 0.61470 (16464) SS BOND : bond 0.00601 ( 6) SS BOND : angle 1.45237 ( 12) hydrogen bonds : bond 0.04787 ( 457) hydrogen bonds : angle 5.07080 ( 1335) link_NAG-ASN : bond 0.00264 ( 6) link_NAG-ASN : angle 2.40898 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 139 time to evaluate : 0.470 Fit side-chains REVERT: A 107 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7047 (mm-30) REVERT: A 128 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: A 286 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: A 415 LYS cc_start: 0.8290 (ttpm) cc_final: 0.7955 (tttp) REVERT: A 585 ASN cc_start: 0.7729 (m-40) cc_final: 0.7377 (m-40) REVERT: A 619 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: B 286 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8679 (pm20) REVERT: B 415 LYS cc_start: 0.8356 (ttpm) cc_final: 0.7987 (tttp) REVERT: B 535 GLU cc_start: 0.8517 (tt0) cc_final: 0.8305 (tt0) REVERT: B 585 ASN cc_start: 0.7638 (m-40) cc_final: 0.7385 (m-40) REVERT: B 619 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8542 (mt-10) REVERT: C 112 ASN cc_start: 0.8506 (m-40) cc_final: 0.8272 (m110) REVERT: C 286 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: C 304 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6557 (mtm180) REVERT: C 349 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7990 (mptt) REVERT: C 415 LYS cc_start: 0.8354 (ttpm) cc_final: 0.7995 (tttp) REVERT: C 585 ASN cc_start: 0.7687 (m-40) cc_final: 0.7399 (m-40) REVERT: C 619 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8521 (mt-10) outliers start: 90 outliers final: 68 residues processed: 206 average time/residue: 0.5583 time to fit residues: 124.8469 Evaluate side-chains 214 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 137 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 TRP Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 539 TRP Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.156409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120746 restraints weight = 10885.907| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.57 r_work: 0.3158 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12132 Z= 0.147 Angle : 0.566 7.883 16494 Z= 0.306 Chirality : 0.044 0.213 1800 Planarity : 0.005 0.053 2139 Dihedral : 8.458 64.925 1827 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 6.70 % Allowed : 16.27 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.23 (0.21), residues: 1431 helix: 1.37 (0.32), residues: 240 sheet: 0.97 (0.24), residues: 456 loop : -0.80 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 505 TYR 0.012 0.001 TYR B 114 PHE 0.018 0.002 PHE C 287 TRP 0.017 0.002 TRP A 539 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00342 (12120) covalent geometry : angle 0.56159 (16464) SS BOND : bond 0.00497 ( 6) SS BOND : angle 1.18918 ( 12) hydrogen bonds : bond 0.04201 ( 457) hydrogen bonds : angle 4.93462 ( 1335) link_NAG-ASN : bond 0.00256 ( 6) link_NAG-ASN : angle 2.15100 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 137 time to evaluate : 0.451 Fit side-chains REVERT: A 107 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7049 (mm-30) REVERT: A 128 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7943 (mm-30) REVERT: A 415 LYS cc_start: 0.8337 (ttpm) cc_final: 0.8011 (tttp) REVERT: A 539 TRP cc_start: 0.7855 (OUTLIER) cc_final: 0.7525 (m-10) REVERT: A 585 ASN cc_start: 0.7697 (m-40) cc_final: 0.7364 (m-40) REVERT: A 619 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8471 (mt-10) REVERT: B 286 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8614 (pm20) REVERT: B 415 LYS cc_start: 0.8351 (ttpm) cc_final: 0.7982 (tttp) REVERT: B 585 ASN cc_start: 0.7619 (m-40) cc_final: 0.7366 (m-40) REVERT: B 619 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8503 (mt-10) REVERT: C 286 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8151 (pm20) REVERT: C 304 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6566 (mtm180) REVERT: C 349 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7977 (mptt) REVERT: C 415 LYS cc_start: 0.8336 (ttpm) cc_final: 0.7986 (tttp) REVERT: C 535 GLU cc_start: 0.8424 (tt0) cc_final: 0.8151 (tp30) REVERT: C 585 ASN cc_start: 0.7636 (m-40) cc_final: 0.7356 (m-40) REVERT: C 619 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8518 (mt-10) outliers start: 84 outliers final: 63 residues processed: 200 average time/residue: 0.5885 time to fit residues: 127.3548 Evaluate side-chains 206 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 134 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 TRP Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 539 TRP Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 131 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.157332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.121812 restraints weight = 10857.422| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.57 r_work: 0.3171 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12132 Z= 0.129 Angle : 0.546 7.514 16494 Z= 0.294 Chirality : 0.043 0.203 1800 Planarity : 0.005 0.053 2139 Dihedral : 8.123 63.138 1823 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 6.30 % Allowed : 16.75 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.32 (0.21), residues: 1431 helix: 1.50 (0.32), residues: 240 sheet: 1.02 (0.24), residues: 456 loop : -0.76 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 505 TYR 0.011 0.001 TYR B 114 PHE 0.017 0.001 PHE C 287 TRP 0.016 0.002 TRP A 539 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00298 (12120) covalent geometry : angle 0.54203 (16464) SS BOND : bond 0.00454 ( 6) SS BOND : angle 1.08060 ( 12) hydrogen bonds : bond 0.03925 ( 457) hydrogen bonds : angle 4.84169 ( 1335) link_NAG-ASN : bond 0.00279 ( 6) link_NAG-ASN : angle 1.98351 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 139 time to evaluate : 0.471 Fit side-chains REVERT: A 107 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7077 (mm-30) REVERT: A 128 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7927 (mm-30) REVERT: A 415 LYS cc_start: 0.8307 (ttpm) cc_final: 0.7984 (tttp) REVERT: A 459 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7813 (m) REVERT: A 539 TRP cc_start: 0.7819 (OUTLIER) cc_final: 0.7472 (m-10) REVERT: A 579 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7460 (p0) REVERT: A 585 ASN cc_start: 0.7681 (m-40) cc_final: 0.7353 (m-40) REVERT: A 619 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8460 (mt-10) REVERT: B 286 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8622 (pm20) REVERT: B 360 ARG cc_start: 0.6036 (mmp-170) cc_final: 0.5754 (mmp-170) REVERT: B 415 LYS cc_start: 0.8334 (ttpm) cc_final: 0.7975 (tttp) REVERT: B 585 ASN cc_start: 0.7610 (m-40) cc_final: 0.7359 (m-40) REVERT: B 619 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: C 107 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6885 (mm-30) REVERT: C 286 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: C 304 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6549 (mtm180) REVERT: C 415 LYS cc_start: 0.8307 (ttpm) cc_final: 0.7929 (tttp) REVERT: C 535 GLU cc_start: 0.8424 (tt0) cc_final: 0.8142 (tp30) REVERT: C 579 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7542 (p0) REVERT: C 585 ASN cc_start: 0.7642 (m-40) cc_final: 0.7365 (m-40) REVERT: C 619 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8504 (mt-10) outliers start: 79 outliers final: 60 residues processed: 197 average time/residue: 0.5825 time to fit residues: 123.9888 Evaluate side-chains 207 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 136 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 TRP Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 539 TRP Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 0.0980 chunk 57 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.157562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.122077 restraints weight = 10870.801| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.57 r_work: 0.3169 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12132 Z= 0.126 Angle : 0.549 7.447 16494 Z= 0.294 Chirality : 0.043 0.203 1800 Planarity : 0.005 0.053 2139 Dihedral : 7.939 62.919 1818 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 5.82 % Allowed : 17.30 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.37 (0.21), residues: 1431 helix: 1.55 (0.32), residues: 240 sheet: 1.06 (0.24), residues: 456 loop : -0.74 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 505 TYR 0.011 0.001 TYR B 114 PHE 0.016 0.001 PHE C 287 TRP 0.016 0.002 TRP A 539 HIS 0.003 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00290 (12120) covalent geometry : angle 0.54445 (16464) SS BOND : bond 0.00432 ( 6) SS BOND : angle 1.03342 ( 12) hydrogen bonds : bond 0.03852 ( 457) hydrogen bonds : angle 4.80774 ( 1335) link_NAG-ASN : bond 0.00288 ( 6) link_NAG-ASN : angle 1.97068 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 137 time to evaluate : 0.400 Fit side-chains REVERT: A 107 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7077 (mm-30) REVERT: A 128 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7927 (mm-30) REVERT: A 409 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5774 (mm) REVERT: A 415 LYS cc_start: 0.8324 (ttpm) cc_final: 0.7992 (tttp) REVERT: A 459 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7805 (m) REVERT: A 539 TRP cc_start: 0.7808 (OUTLIER) cc_final: 0.7459 (m-10) REVERT: A 579 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7476 (p0) REVERT: A 585 ASN cc_start: 0.7693 (m-40) cc_final: 0.7353 (m-40) REVERT: A 619 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8452 (mt-10) REVERT: B 286 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8622 (pm20) REVERT: B 415 LYS cc_start: 0.8327 (ttpm) cc_final: 0.7974 (tttp) REVERT: B 579 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7562 (p0) REVERT: B 585 ASN cc_start: 0.7512 (m-40) cc_final: 0.7269 (m-40) REVERT: B 619 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8500 (mt-10) REVERT: C 107 GLU cc_start: 0.7614 (mt-10) cc_final: 0.6887 (mm-30) REVERT: C 286 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8131 (pm20) REVERT: C 304 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6554 (mtm180) REVERT: C 415 LYS cc_start: 0.8286 (ttpm) cc_final: 0.7903 (tttp) REVERT: C 535 GLU cc_start: 0.8419 (tt0) cc_final: 0.8131 (tp30) REVERT: C 579 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7528 (p0) REVERT: C 585 ASN cc_start: 0.7636 (m-40) cc_final: 0.7362 (m-40) REVERT: C 619 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8498 (mt-10) outliers start: 73 outliers final: 54 residues processed: 191 average time/residue: 0.5856 time to fit residues: 120.6786 Evaluate side-chains 201 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 134 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 TRP Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 539 TRP Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 20 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 98 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.158265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122442 restraints weight = 11006.894| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.60 r_work: 0.3176 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12132 Z= 0.116 Angle : 0.539 7.145 16494 Z= 0.288 Chirality : 0.042 0.197 1800 Planarity : 0.005 0.058 2139 Dihedral : 7.687 62.398 1816 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 5.02 % Allowed : 18.02 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.43 (0.22), residues: 1431 helix: 1.64 (0.32), residues: 240 sheet: 1.11 (0.24), residues: 456 loop : -0.72 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 505 TYR 0.010 0.001 TYR B 114 PHE 0.015 0.001 PHE C 287 TRP 0.015 0.002 TRP A 539 HIS 0.003 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00266 (12120) covalent geometry : angle 0.53567 (16464) SS BOND : bond 0.00398 ( 6) SS BOND : angle 0.97177 ( 12) hydrogen bonds : bond 0.03669 ( 457) hydrogen bonds : angle 4.74878 ( 1335) link_NAG-ASN : bond 0.00306 ( 6) link_NAG-ASN : angle 1.88190 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 137 time to evaluate : 0.378 Fit side-chains REVERT: A 107 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7079 (mm-30) REVERT: A 128 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: A 409 LEU cc_start: 0.5881 (OUTLIER) cc_final: 0.5675 (mm) REVERT: A 415 LYS cc_start: 0.8317 (ttpm) cc_final: 0.7977 (tttp) REVERT: A 459 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7791 (m) REVERT: A 539 TRP cc_start: 0.7767 (OUTLIER) cc_final: 0.7441 (m-10) REVERT: A 585 ASN cc_start: 0.7667 (m-40) cc_final: 0.7338 (m-40) REVERT: A 619 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8437 (mt-10) REVERT: B 286 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8642 (pm20) REVERT: B 360 ARG cc_start: 0.6079 (mmp-170) cc_final: 0.5838 (mmp-170) REVERT: B 415 LYS cc_start: 0.8365 (ttpm) cc_final: 0.7988 (tttp) REVERT: B 459 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.7861 (m) REVERT: B 539 TRP cc_start: 0.7760 (OUTLIER) cc_final: 0.7422 (m-10) REVERT: B 585 ASN cc_start: 0.7511 (m-40) cc_final: 0.7267 (m-40) REVERT: B 619 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8487 (mt-10) REVERT: C 107 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6879 (mm-30) REVERT: C 286 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: C 304 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6571 (mtm180) REVERT: C 349 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8053 (mptt) REVERT: C 415 LYS cc_start: 0.8272 (ttpm) cc_final: 0.7890 (tttp) REVERT: C 535 GLU cc_start: 0.8402 (tt0) cc_final: 0.8114 (tp30) REVERT: C 585 ASN cc_start: 0.7625 (m-40) cc_final: 0.7350 (m-40) REVERT: C 619 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8485 (mt-10) outliers start: 63 outliers final: 47 residues processed: 184 average time/residue: 0.5901 time to fit residues: 117.2671 Evaluate side-chains 196 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 539 TRP Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 539 TRP Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 539 TRP Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.155003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.119064 restraints weight = 10948.634| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.58 r_work: 0.3126 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12132 Z= 0.221 Angle : 0.661 8.789 16494 Z= 0.354 Chirality : 0.048 0.238 1800 Planarity : 0.006 0.066 2139 Dihedral : 8.183 65.788 1808 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 5.66 % Allowed : 17.22 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.20 (0.21), residues: 1431 helix: 1.28 (0.32), residues: 240 sheet: 0.98 (0.24), residues: 456 loop : -0.83 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 505 TYR 0.016 0.002 TYR B 114 PHE 0.021 0.002 PHE B 287 TRP 0.020 0.003 TRP B 539 HIS 0.004 0.001 HIS A 657 Details of bonding type rmsd covalent geometry : bond 0.00529 (12120) covalent geometry : angle 0.65577 (16464) SS BOND : bond 0.00620 ( 6) SS BOND : angle 1.47341 ( 12) hydrogen bonds : bond 0.04881 ( 457) hydrogen bonds : angle 5.04481 ( 1335) link_NAG-ASN : bond 0.00290 ( 6) link_NAG-ASN : angle 2.43440 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4872.76 seconds wall clock time: 83 minutes 28.37 seconds (5008.37 seconds total)