Starting phenix.real_space_refine on Wed Mar 4 05:25:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xa9_33088/03_2026/7xa9_33088.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xa9_33088/03_2026/7xa9_33088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xa9_33088/03_2026/7xa9_33088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xa9_33088/03_2026/7xa9_33088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xa9_33088/03_2026/7xa9_33088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xa9_33088/03_2026/7xa9_33088.map" } resolution = 2.84 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= -0.000 sd= 0.026 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 7140 2.51 5 N 1844 2.21 5 O 1978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11028 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5470 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 29, 'TRANS': 672} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' MG': 1, 'ATP': 1, 'NO3': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: B Time building chain proxies: 4.38, per 1000 atoms: 0.40 Number of scatterers: 11028 At special positions: 0 Unit cell: (77.9, 104.14, 104.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 2 11.99 O 1978 8.00 N 1844 7.00 C 7140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 306 " distance=2.35 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 419 " distance=2.36 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 405 " distance=2.29 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 306 " distance=2.35 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 419 " distance=2.36 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 405 " distance=2.29 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 564.4 milliseconds 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 61.7% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.689A pdb=" N ARG A 74 " --> pdb=" O TRP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 125 removed outlier: 3.586A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 154 Processing helix chain 'A' and resid 155 through 158 removed outlier: 3.654A pdb=" N ALA A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 158' Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.745A pdb=" N ALA A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 220 removed outlier: 3.611A pdb=" N VAL A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.550A pdb=" N LEU A 232 " --> pdb=" O TRP A 229 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR A 234 " --> pdb=" O TRP A 231 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN A 236 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.721A pdb=" N ASP A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 276 through 300 removed outlier: 3.915A pdb=" N ARG A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 331 through 364 removed outlier: 3.603A pdb=" N ILE A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 387 removed outlier: 3.789A pdb=" N VAL A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.611A pdb=" N ARG A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 470 Processing helix chain 'A' and resid 479 through 498 removed outlier: 3.833A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 523 removed outlier: 3.642A pdb=" N VAL A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 537 Processing helix chain 'A' and resid 541 through 557 Processing helix chain 'A' and resid 562 through 571 removed outlier: 3.571A pdb=" N ILE A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 3.649A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 643 through 653 removed outlier: 3.535A pdb=" N ARG A 653 " --> pdb=" O VAL A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.560A pdb=" N ALA A 677 " --> pdb=" O PRO A 673 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 678 " --> pdb=" O VAL A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 694 removed outlier: 3.744A pdb=" N GLN A 694 " --> pdb=" O SER A 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 694' Processing helix chain 'A' and resid 715 through 726 removed outlier: 3.561A pdb=" N VAL A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 755 through 763 removed outlier: 3.546A pdb=" N ALA A 762 " --> pdb=" O ASN A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.689A pdb=" N ARG B 74 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 125 removed outlier: 3.586A pdb=" N PHE B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 154 Processing helix chain 'B' and resid 155 through 158 removed outlier: 3.654A pdb=" N ALA B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 158' Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 179 through 196 removed outlier: 3.745A pdb=" N ALA B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 220 removed outlier: 3.611A pdb=" N VAL B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 236 removed outlier: 3.550A pdb=" N LEU B 232 " --> pdb=" O TRP B 229 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR B 234 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 236 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.721A pdb=" N ASP B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 276 through 300 removed outlier: 3.915A pdb=" N ARG B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 330 Processing helix chain 'B' and resid 331 through 364 removed outlier: 3.603A pdb=" N ILE B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 387 removed outlier: 3.789A pdb=" N VAL B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 391 Processing helix chain 'B' and resid 436 through 443 removed outlier: 3.611A pdb=" N ARG B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 470 Processing helix chain 'B' and resid 479 through 498 removed outlier: 3.833A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 523 removed outlier: 3.642A pdb=" N VAL B 511 " --> pdb=" O GLY B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 537 Processing helix chain 'B' and resid 541 through 557 Processing helix chain 'B' and resid 562 through 571 removed outlier: 3.571A pdb=" N ILE B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 595 removed outlier: 3.649A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 643 through 653 removed outlier: 3.535A pdb=" N ARG B 653 " --> pdb=" O VAL B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.560A pdb=" N ALA B 677 " --> pdb=" O PRO B 673 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B 678 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 694 removed outlier: 3.744A pdb=" N GLN B 694 " --> pdb=" O SER B 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 691 through 694' Processing helix chain 'B' and resid 715 through 726 removed outlier: 3.561A pdb=" N VAL B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 Processing helix chain 'B' and resid 755 through 763 removed outlier: 3.546A pdb=" N ALA B 762 " --> pdb=" O ASN B 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 396 Processing sheet with id=AA2, first strand: chain 'A' and resid 602 through 603 removed outlier: 6.626A pdb=" N LEU A 602 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 639 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 605 through 607 Processing sheet with id=AA4, first strand: chain 'A' and resid 709 through 710 Processing sheet with id=AA5, first strand: chain 'B' and resid 395 through 396 Processing sheet with id=AA6, first strand: chain 'B' and resid 602 through 603 removed outlier: 6.626A pdb=" N LEU B 602 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 639 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 605 through 607 Processing sheet with id=AA8, first strand: chain 'B' and resid 709 through 710 612 hydrogen bonds defined for protein. 1794 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: 1.28 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: 1794 1.32 - 1.44: 3034 1.44 - 1.56: 6346 1.56 - 1.69: 12 1.69 - 1.81: 90 Bond restraints: 11276 Sorted by residual: bond pdb=" C GLN A 416 " pdb=" N PHE A 417 " ideal model delta sigma weight residual 1.334 1.440 -0.106 1.41e-02 5.03e+03 5.69e+01 bond pdb=" C GLN B 416 " pdb=" N PHE B 417 " ideal model delta sigma weight residual 1.334 1.440 -0.106 1.41e-02 5.03e+03 5.69e+01 bond pdb=" C5 ATP B 904 " pdb=" C6 ATP B 904 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.69e+01 bond pdb=" C5 ATP A 904 " pdb=" C6 ATP A 904 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.69e+01 bond pdb=" C4 ATP B 904 " pdb=" C5 ATP B 904 " ideal model delta sigma weight residual 1.388 1.452 -0.064 1.00e-02 1.00e+04 4.14e+01 ... (remaining 11271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 14770 3.19 - 6.39: 498 6.39 - 9.58: 70 9.58 - 12.78: 6 12.78 - 15.97: 4 Bond angle restraints: 15348 Sorted by residual: angle pdb=" PA ATP A 904 " pdb=" O3A ATP A 904 " pdb=" PB ATP A 904 " ideal model delta sigma weight residual 136.83 120.86 15.97 1.00e+00 1.00e+00 2.55e+02 angle pdb=" PA ATP B 904 " pdb=" O3A ATP B 904 " pdb=" PB ATP B 904 " ideal model delta sigma weight residual 136.83 120.86 15.97 1.00e+00 1.00e+00 2.55e+02 angle pdb=" PB ATP B 904 " pdb=" O3B ATP B 904 " pdb=" PG ATP B 904 " ideal model delta sigma weight residual 139.87 125.63 14.24 1.00e+00 1.00e+00 2.03e+02 angle pdb=" PB ATP A 904 " pdb=" O3B ATP A 904 " pdb=" PG ATP A 904 " ideal model delta sigma weight residual 139.87 125.63 14.24 1.00e+00 1.00e+00 2.03e+02 angle pdb=" N LYS A 202 " pdb=" CA LYS A 202 " pdb=" C LYS A 202 " ideal model delta sigma weight residual 112.59 102.56 10.03 1.22e+00 6.72e-01 6.76e+01 ... (remaining 15343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5730 17.71 - 35.43: 728 35.43 - 53.14: 130 53.14 - 70.85: 32 70.85 - 88.57: 18 Dihedral angle restraints: 6638 sinusoidal: 2622 harmonic: 4016 Sorted by residual: dihedral pdb=" CB CYS A 301 " pdb=" SG CYS A 301 " pdb=" SG CYS A 306 " pdb=" CB CYS A 306 " ideal model delta sinusoidal sigma weight residual -86.00 -30.10 -55.90 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS B 301 " pdb=" SG CYS B 301 " pdb=" SG CYS B 306 " pdb=" CB CYS B 306 " ideal model delta sinusoidal sigma weight residual -86.00 -30.10 -55.90 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CA GLU A 270 " pdb=" C GLU A 270 " pdb=" N VAL A 271 " pdb=" CA VAL A 271 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 6635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1022 0.047 - 0.095: 524 0.095 - 0.142: 164 0.142 - 0.190: 62 0.190 - 0.237: 22 Chirality restraints: 1794 Sorted by residual: chirality pdb=" CA LYS B 202 " pdb=" N LYS B 202 " pdb=" C LYS B 202 " pdb=" CB LYS B 202 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LYS A 202 " pdb=" N LYS A 202 " pdb=" C LYS A 202 " pdb=" CB LYS A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL A 291 " pdb=" CA VAL A 291 " pdb=" CG1 VAL A 291 " pdb=" CG2 VAL A 291 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1791 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 278 " -0.025 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C ALA B 278 " 0.084 2.00e-02 2.50e+03 pdb=" O ALA B 278 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU B 279 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 278 " -0.025 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C ALA A 278 " 0.084 2.00e-02 2.50e+03 pdb=" O ALA A 278 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU A 279 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 289 " -0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C VAL A 289 " 0.075 2.00e-02 2.50e+03 pdb=" O VAL A 289 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL A 290 " -0.026 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 94 2.53 - 3.12: 6798 3.12 - 3.72: 18514 3.72 - 4.31: 27487 4.31 - 4.90: 44633 Nonbonded interactions: 97526 Sorted by model distance: nonbonded pdb=" OE1 GLU A 55 " pdb="MG MG A 905 " model vdw 1.938 2.170 nonbonded pdb=" OE1 GLU B 55 " pdb="MG MG B 905 " model vdw 1.938 2.170 nonbonded pdb=" O2B ATP A 904 " pdb="MG MG A 905 " model vdw 2.121 2.170 nonbonded pdb=" O2B ATP B 904 " pdb="MG MG B 905 " model vdw 2.121 2.170 nonbonded pdb=" OD2 ASP A 753 " pdb=" O2' ATP A 904 " model vdw 2.327 3.040 ... (remaining 97521 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 11.940 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.180 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.013 0.333 11282 Z= 0.642 Angle : 1.366 15.970 15360 Z= 0.807 Chirality : 0.067 0.237 1794 Planarity : 0.011 0.094 1914 Dihedral : 16.618 88.565 4044 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.17 % Allowed : 22.15 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.15), residues: 1392 helix: -3.91 (0.09), residues: 820 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 523 TYR 0.031 0.003 TYR A 490 PHE 0.035 0.004 PHE A 317 TRP 0.021 0.003 TRP A 274 HIS 0.013 0.002 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.01037 (11276) covalent geometry : angle 1.33369 (15348) SS BOND : bond 0.30545 ( 6) SS BOND : angle 10.61625 ( 12) hydrogen bonds : bond 0.19555 ( 612) hydrogen bonds : angle 9.29327 ( 1794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.288 Fit side-chains REVERT: A 122 TYR cc_start: 0.7860 (m-80) cc_final: 0.7430 (m-80) REVERT: A 268 LEU cc_start: 0.8651 (tt) cc_final: 0.8428 (tp) REVERT: A 276 ARG cc_start: 0.8300 (mtm180) cc_final: 0.8075 (mtm180) REVERT: A 449 ASN cc_start: 0.7717 (m-40) cc_final: 0.7413 (m-40) REVERT: B 122 TYR cc_start: 0.7860 (m-80) cc_final: 0.7429 (m-80) REVERT: B 268 LEU cc_start: 0.8650 (tt) cc_final: 0.8428 (tp) REVERT: B 276 ARG cc_start: 0.8296 (mtm180) cc_final: 0.8070 (mtm180) REVERT: B 449 ASN cc_start: 0.7715 (m-40) cc_final: 0.7413 (m-40) outliers start: 2 outliers final: 2 residues processed: 198 average time/residue: 0.5027 time to fit residues: 108.0856 Evaluate side-chains 158 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain B residue 483 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 537 ASN A 620 HIS B 170 ASN B 537 ASN B 620 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.157295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140248 restraints weight = 11771.124| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.47 r_work: 0.3444 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11282 Z= 0.186 Angle : 0.636 6.308 15360 Z= 0.336 Chirality : 0.042 0.133 1794 Planarity : 0.006 0.062 1914 Dihedral : 9.492 84.709 1574 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.35 % Allowed : 22.32 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.20), residues: 1392 helix: -1.25 (0.16), residues: 828 sheet: None (None), residues: 0 loop : -1.36 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.016 0.001 TYR B 463 PHE 0.018 0.002 PHE A 317 TRP 0.010 0.001 TRP A 87 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00424 (11276) covalent geometry : angle 0.63447 (15348) SS BOND : bond 0.00635 ( 6) SS BOND : angle 1.47221 ( 12) hydrogen bonds : bond 0.04844 ( 612) hydrogen bonds : angle 5.41010 ( 1794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.336 Fit side-chains REVERT: A 122 TYR cc_start: 0.8135 (m-80) cc_final: 0.7772 (m-80) REVERT: A 237 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7857 (p0) REVERT: A 365 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7883 (mtmt) REVERT: A 570 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 636 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: A 693 MET cc_start: 0.8602 (mmm) cc_final: 0.8300 (tpt) REVERT: B 122 TYR cc_start: 0.8135 (m-80) cc_final: 0.7766 (m-80) REVERT: B 237 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7865 (p0) REVERT: B 365 LYS cc_start: 0.8242 (mtpp) cc_final: 0.7900 (mtmt) REVERT: B 570 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8279 (tt) REVERT: B 636 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: B 693 MET cc_start: 0.8609 (mmm) cc_final: 0.8308 (tpt) outliers start: 28 outliers final: 12 residues processed: 174 average time/residue: 0.4604 time to fit residues: 87.5028 Evaluate side-chains 152 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 95 optimal weight: 0.0970 chunk 53 optimal weight: 0.2980 chunk 110 optimal weight: 0.3980 chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS B 327 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.157161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139990 restraints weight = 11790.168| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.47 r_work: 0.3448 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11282 Z= 0.164 Angle : 0.565 5.584 15360 Z= 0.294 Chirality : 0.040 0.125 1794 Planarity : 0.005 0.053 1914 Dihedral : 8.303 72.957 1570 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.02 % Allowed : 20.13 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1392 helix: -0.08 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -1.03 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 653 TYR 0.010 0.001 TYR A 509 PHE 0.017 0.002 PHE A 459 TRP 0.010 0.001 TRP A 87 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00374 (11276) covalent geometry : angle 0.56422 (15348) SS BOND : bond 0.00443 ( 6) SS BOND : angle 1.21882 ( 12) hydrogen bonds : bond 0.04422 ( 612) hydrogen bonds : angle 4.93431 ( 1794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.297 Fit side-chains REVERT: A 55 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: A 122 TYR cc_start: 0.8099 (m-80) cc_final: 0.7713 (m-80) REVERT: A 237 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7889 (p0) REVERT: A 365 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7921 (mttt) REVERT: A 483 ILE cc_start: 0.8470 (mt) cc_final: 0.8270 (mt) REVERT: B 55 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: B 122 TYR cc_start: 0.8096 (m-80) cc_final: 0.7707 (m-80) REVERT: B 237 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7896 (p0) REVERT: B 365 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7941 (mttt) REVERT: B 483 ILE cc_start: 0.8461 (mt) cc_final: 0.8260 (mt) outliers start: 36 outliers final: 18 residues processed: 174 average time/residue: 0.4259 time to fit residues: 81.6799 Evaluate side-chains 158 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 672 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 13 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 128 optimal weight: 0.0670 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 538 ASN B 327 HIS B 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137787 restraints weight = 11854.317| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.48 r_work: 0.3398 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11282 Z= 0.205 Angle : 0.589 5.656 15360 Z= 0.303 Chirality : 0.042 0.125 1794 Planarity : 0.005 0.050 1914 Dihedral : 8.079 74.004 1570 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.19 % Allowed : 20.13 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.22), residues: 1392 helix: 0.29 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -0.84 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 679 TYR 0.012 0.002 TYR B 463 PHE 0.017 0.002 PHE B 459 TRP 0.009 0.001 TRP A 87 HIS 0.003 0.001 HIS A 645 Details of bonding type rmsd covalent geometry : bond 0.00488 (11276) covalent geometry : angle 0.58852 (15348) SS BOND : bond 0.00374 ( 6) SS BOND : angle 1.14466 ( 12) hydrogen bonds : bond 0.04504 ( 612) hydrogen bonds : angle 4.87139 ( 1794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 0.385 Fit side-chains REVERT: A 55 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: A 85 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 122 TYR cc_start: 0.8093 (m-80) cc_final: 0.7739 (m-80) REVERT: A 237 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7841 (p0) REVERT: A 365 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7864 (mttt) REVERT: A 393 GLU cc_start: 0.7589 (tt0) cc_final: 0.6862 (pm20) REVERT: A 636 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: A 693 MET cc_start: 0.8688 (mmm) cc_final: 0.8435 (mmm) REVERT: B 55 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: B 85 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8419 (mp) REVERT: B 122 TYR cc_start: 0.8103 (m-80) cc_final: 0.7750 (m-80) REVERT: B 237 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7838 (p0) REVERT: B 365 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7880 (mttt) REVERT: B 393 GLU cc_start: 0.7598 (tt0) cc_final: 0.6871 (pm20) REVERT: B 636 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: B 693 MET cc_start: 0.8684 (mmm) cc_final: 0.8434 (mmm) outliers start: 50 outliers final: 14 residues processed: 176 average time/residue: 0.4402 time to fit residues: 85.1985 Evaluate side-chains 158 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 93 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 137 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS B 327 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.155227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137942 restraints weight = 11598.990| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.47 r_work: 0.3496 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11282 Z= 0.185 Angle : 0.566 5.300 15360 Z= 0.292 Chirality : 0.042 0.121 1794 Planarity : 0.005 0.046 1914 Dihedral : 7.777 74.476 1570 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.52 % Allowed : 19.97 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.22), residues: 1392 helix: 0.50 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.87 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.011 0.001 TYR B 463 PHE 0.017 0.002 PHE A 459 TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS B 645 Details of bonding type rmsd covalent geometry : bond 0.00438 (11276) covalent geometry : angle 0.56523 (15348) SS BOND : bond 0.00384 ( 6) SS BOND : angle 0.98699 ( 12) hydrogen bonds : bond 0.04387 ( 612) hydrogen bonds : angle 4.77070 ( 1794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.386 Fit side-chains REVERT: A 55 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: A 83 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8339 (mp) REVERT: A 122 TYR cc_start: 0.8097 (m-80) cc_final: 0.7789 (m-80) REVERT: A 365 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7843 (mttt) REVERT: A 393 GLU cc_start: 0.7562 (tt0) cc_final: 0.6989 (pm20) REVERT: A 636 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: B 55 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: B 83 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8353 (mp) REVERT: B 122 TYR cc_start: 0.8091 (m-80) cc_final: 0.7784 (m-80) REVERT: B 365 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7859 (mttt) REVERT: B 393 GLU cc_start: 0.7597 (tt0) cc_final: 0.6997 (pm20) REVERT: B 636 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7230 (tt0) outliers start: 42 outliers final: 16 residues processed: 174 average time/residue: 0.4332 time to fit residues: 82.9513 Evaluate side-chains 162 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 327 HIS B 237 ASN B 327 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.154340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137188 restraints weight = 11735.136| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.45 r_work: 0.3393 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11282 Z= 0.202 Angle : 0.584 5.603 15360 Z= 0.300 Chirality : 0.042 0.126 1794 Planarity : 0.005 0.048 1914 Dihedral : 7.647 75.580 1570 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.19 % Allowed : 19.13 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.22), residues: 1392 helix: 0.59 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.78 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 239 TYR 0.012 0.002 TYR B 463 PHE 0.017 0.002 PHE B 459 TRP 0.009 0.001 TRP B 87 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00485 (11276) covalent geometry : angle 0.58389 (15348) SS BOND : bond 0.00469 ( 6) SS BOND : angle 0.97632 ( 12) hydrogen bonds : bond 0.04478 ( 612) hydrogen bonds : angle 4.78394 ( 1794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 0.289 Fit side-chains REVERT: A 55 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: A 63 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: A 83 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8304 (mp) REVERT: A 86 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7382 (mmtp) REVERT: A 103 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7867 (tp) REVERT: A 122 TYR cc_start: 0.8086 (m-80) cc_final: 0.7789 (m-80) REVERT: A 365 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7807 (mttt) REVERT: A 393 GLU cc_start: 0.7535 (tt0) cc_final: 0.6845 (pm20) REVERT: A 636 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: A 693 MET cc_start: 0.8621 (mmm) cc_final: 0.8314 (mmm) REVERT: B 55 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: B 63 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8347 (mt-10) REVERT: B 83 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8311 (mp) REVERT: B 86 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7372 (mmtp) REVERT: B 103 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7889 (tp) REVERT: B 122 TYR cc_start: 0.8089 (m-80) cc_final: 0.7792 (m-80) REVERT: B 365 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7796 (mttt) REVERT: B 393 GLU cc_start: 0.7561 (tt0) cc_final: 0.6872 (pm20) REVERT: B 636 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: B 693 MET cc_start: 0.8623 (mmm) cc_final: 0.8327 (mmm) outliers start: 50 outliers final: 18 residues processed: 184 average time/residue: 0.4604 time to fit residues: 92.8817 Evaluate side-chains 168 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 72 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 139 optimal weight: 0.0870 chunk 75 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS B 327 HIS B 752 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.155712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139545 restraints weight = 11607.029| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.32 r_work: 0.3461 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11282 Z= 0.164 Angle : 0.555 6.160 15360 Z= 0.286 Chirality : 0.041 0.123 1794 Planarity : 0.004 0.045 1914 Dihedral : 7.374 75.916 1570 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.19 % Allowed : 19.88 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.22), residues: 1392 helix: 0.79 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.75 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 653 TYR 0.010 0.001 TYR A 463 PHE 0.016 0.002 PHE B 459 TRP 0.009 0.001 TRP B 87 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00385 (11276) covalent geometry : angle 0.55453 (15348) SS BOND : bond 0.00315 ( 6) SS BOND : angle 0.87647 ( 12) hydrogen bonds : bond 0.04303 ( 612) hydrogen bonds : angle 4.67770 ( 1794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.333 Fit side-chains REVERT: A 55 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7441 (mm-30) REVERT: A 63 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: A 86 LYS cc_start: 0.8102 (ptpt) cc_final: 0.7451 (mmtp) REVERT: A 103 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7887 (tp) REVERT: A 109 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7700 (mp0) REVERT: A 122 TYR cc_start: 0.8059 (m-80) cc_final: 0.7723 (m-80) REVERT: A 365 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7845 (mttt) REVERT: A 393 GLU cc_start: 0.7518 (tt0) cc_final: 0.6839 (mp0) REVERT: A 636 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: A 685 ASP cc_start: 0.6242 (OUTLIER) cc_final: 0.6020 (p0) REVERT: B 55 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7451 (mm-30) REVERT: B 63 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: B 86 LYS cc_start: 0.8083 (ptpt) cc_final: 0.7432 (mmtp) REVERT: B 103 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7896 (tp) REVERT: B 109 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7713 (mp0) REVERT: B 122 TYR cc_start: 0.8058 (m-80) cc_final: 0.7720 (m-80) REVERT: B 365 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7844 (mttt) REVERT: B 393 GLU cc_start: 0.7556 (tt0) cc_final: 0.6855 (mp0) REVERT: B 636 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: B 685 ASP cc_start: 0.6230 (OUTLIER) cc_final: 0.6004 (p0) outliers start: 38 outliers final: 16 residues processed: 183 average time/residue: 0.4393 time to fit residues: 88.2110 Evaluate side-chains 168 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 685 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 88 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 752 GLN B 327 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139399 restraints weight = 11641.280| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.23 r_work: 0.3467 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11282 Z= 0.202 Angle : 0.585 5.482 15360 Z= 0.299 Chirality : 0.043 0.156 1794 Planarity : 0.005 0.044 1914 Dihedral : 7.448 75.661 1570 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.02 % Allowed : 20.89 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.22), residues: 1392 helix: 0.87 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.72 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 492 TYR 0.011 0.001 TYR B 463 PHE 0.017 0.002 PHE B 459 TRP 0.009 0.001 TRP B 87 HIS 0.005 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00485 (11276) covalent geometry : angle 0.58430 (15348) SS BOND : bond 0.00400 ( 6) SS BOND : angle 0.94817 ( 12) hydrogen bonds : bond 0.04460 ( 612) hydrogen bonds : angle 4.76805 ( 1794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.404 Fit side-chains REVERT: A 55 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7290 (mm-30) REVERT: A 63 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: A 86 LYS cc_start: 0.7912 (ptpt) cc_final: 0.7127 (mmtp) REVERT: A 103 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7748 (tp) REVERT: A 122 TYR cc_start: 0.7965 (m-80) cc_final: 0.7669 (m-80) REVERT: A 365 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7780 (mttt) REVERT: A 393 GLU cc_start: 0.7416 (tt0) cc_final: 0.6686 (pm20) REVERT: A 636 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: A 685 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.6043 (p0) REVERT: B 55 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7281 (mm-30) REVERT: B 63 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: B 86 LYS cc_start: 0.7895 (ptpt) cc_final: 0.7108 (mmtp) REVERT: B 103 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7761 (tp) REVERT: B 122 TYR cc_start: 0.7967 (m-80) cc_final: 0.7670 (m-80) REVERT: B 365 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7777 (mttt) REVERT: B 393 GLU cc_start: 0.7447 (tt0) cc_final: 0.6694 (pm20) REVERT: B 636 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7112 (tt0) REVERT: B 685 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.6034 (p0) outliers start: 36 outliers final: 20 residues processed: 167 average time/residue: 0.4349 time to fit residues: 80.0207 Evaluate side-chains 170 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 41 optimal weight: 0.0870 chunk 23 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS B 327 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.154698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139217 restraints weight = 11623.947| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.24 r_work: 0.3461 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11282 Z= 0.199 Angle : 0.582 5.454 15360 Z= 0.299 Chirality : 0.042 0.140 1794 Planarity : 0.004 0.044 1914 Dihedral : 7.454 75.632 1570 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.10 % Allowed : 20.97 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.31 (0.22), residues: 1392 helix: 0.86 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.69 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 724 TYR 0.011 0.001 TYR A 463 PHE 0.017 0.002 PHE A 459 TRP 0.008 0.001 TRP B 87 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00478 (11276) covalent geometry : angle 0.58201 (15348) SS BOND : bond 0.00431 ( 6) SS BOND : angle 0.94791 ( 12) hydrogen bonds : bond 0.04462 ( 612) hydrogen bonds : angle 4.77866 ( 1794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: A 63 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: A 86 LYS cc_start: 0.7865 (ptpt) cc_final: 0.7105 (mmtp) REVERT: A 103 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7737 (tp) REVERT: A 109 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7483 (mp0) REVERT: A 122 TYR cc_start: 0.7965 (m-80) cc_final: 0.7680 (m-80) REVERT: A 365 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7770 (mttt) REVERT: A 393 GLU cc_start: 0.7426 (tt0) cc_final: 0.6666 (pm20) REVERT: A 636 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7131 (tt0) REVERT: A 685 ASP cc_start: 0.6324 (OUTLIER) cc_final: 0.6082 (p0) REVERT: B 55 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: B 63 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: B 86 LYS cc_start: 0.7846 (ptpt) cc_final: 0.7089 (mmtp) REVERT: B 103 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7750 (tp) REVERT: B 109 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7481 (mp0) REVERT: B 122 TYR cc_start: 0.7961 (m-80) cc_final: 0.7676 (m-80) REVERT: B 365 LYS cc_start: 0.8053 (mtpp) cc_final: 0.7773 (mttt) REVERT: B 393 GLU cc_start: 0.7455 (tt0) cc_final: 0.6672 (pm20) REVERT: B 636 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: B 685 ASP cc_start: 0.6318 (OUTLIER) cc_final: 0.6072 (p0) outliers start: 37 outliers final: 20 residues processed: 167 average time/residue: 0.4387 time to fit residues: 80.5617 Evaluate side-chains 171 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 79 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 139 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 134 optimal weight: 0.0980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS B 327 HIS B 694 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.156849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141571 restraints weight = 11649.527| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.22 r_work: 0.3490 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11282 Z= 0.150 Angle : 0.543 5.127 15360 Z= 0.280 Chirality : 0.041 0.137 1794 Planarity : 0.004 0.044 1914 Dihedral : 7.180 75.438 1570 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.68 % Allowed : 21.14 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.22), residues: 1392 helix: 1.03 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.60 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 653 TYR 0.010 0.001 TYR A 490 PHE 0.015 0.001 PHE B 459 TRP 0.009 0.001 TRP B 87 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00350 (11276) covalent geometry : angle 0.54254 (15348) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.78947 ( 12) hydrogen bonds : bond 0.04230 ( 612) hydrogen bonds : angle 4.63195 ( 1794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7225 (mm-30) REVERT: A 63 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: A 86 LYS cc_start: 0.7807 (ptpt) cc_final: 0.7111 (mmtp) REVERT: A 103 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7751 (tp) REVERT: A 122 TYR cc_start: 0.7920 (m-80) cc_final: 0.7598 (m-80) REVERT: A 276 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7745 (ptt-90) REVERT: A 365 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7669 (mttt) REVERT: A 393 GLU cc_start: 0.7375 (tt0) cc_final: 0.6599 (pm20) REVERT: A 636 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: A 679 ARG cc_start: 0.7973 (mmp-170) cc_final: 0.7743 (mmp-170) REVERT: A 685 ASP cc_start: 0.6294 (OUTLIER) cc_final: 0.6076 (p0) REVERT: B 55 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7235 (mm-30) REVERT: B 63 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: B 86 LYS cc_start: 0.7796 (ptpt) cc_final: 0.7108 (mmtp) REVERT: B 103 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7764 (tp) REVERT: B 122 TYR cc_start: 0.7923 (m-80) cc_final: 0.7604 (m-80) REVERT: B 365 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7687 (mttt) REVERT: B 393 GLU cc_start: 0.7402 (tt0) cc_final: 0.6596 (pm20) REVERT: B 636 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7054 (tt0) REVERT: B 679 ARG cc_start: 0.7979 (mmp-170) cc_final: 0.7752 (mmp-170) REVERT: B 685 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.6062 (p0) outliers start: 32 outliers final: 18 residues processed: 161 average time/residue: 0.4864 time to fit residues: 85.3240 Evaluate side-chains 165 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 36 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 111 optimal weight: 0.0980 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 75 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 694 GLN B 694 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.141060 restraints weight = 11706.267| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.24 r_work: 0.3444 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11282 Z= 0.158 Angle : 0.570 9.128 15360 Z= 0.288 Chirality : 0.041 0.135 1794 Planarity : 0.004 0.043 1914 Dihedral : 7.171 75.148 1570 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.60 % Allowed : 21.06 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.22), residues: 1392 helix: 1.07 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.53 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 276 TYR 0.010 0.001 TYR A 490 PHE 0.015 0.002 PHE A 459 TRP 0.010 0.001 TRP B 275 HIS 0.002 0.001 HIS A 645 Details of bonding type rmsd covalent geometry : bond 0.00372 (11276) covalent geometry : angle 0.57004 (15348) SS BOND : bond 0.00316 ( 6) SS BOND : angle 0.83562 ( 12) hydrogen bonds : bond 0.04264 ( 612) hydrogen bonds : angle 4.63190 ( 1794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3069.66 seconds wall clock time: 53 minutes 24.52 seconds (3204.52 seconds total)