Starting phenix.real_space_refine on Fri Jul 3 00:33:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xa9_33088/07_2026/7xa9_33088.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xa9_33088/07_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_33088/07_2026/7xa9_33088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xa9_33088/07_2026/7xa9_33088.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xa9_33088/07_2026/7xa9_33088.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xa9_33088/07_2026/7xa9_33088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xa9_33088/07_2026/7xa9_33088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xa9_33088/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 4.55, per 1000 atoms: 0.41 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: 0.64 Conformation dependent library (CDL) restraints added in 404.7 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: 0.20 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: 2.09 Time building geometry restraints manager: 0.83 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: 5710 17.71 - 35.43: 702 35.43 - 53.14: 128 53.14 - 70.85: 24 70.85 - 88.57: 12 Dihedral angle restraints: 6576 sinusoidal: 2560 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 6573 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: 0.01 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: 11.590 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: 0.140 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.570 Find NCS groups from input model: 0.070 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:8.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 16.010 88.565 3982 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/Z covalent geometry : bond 0.01037 / 0.54 (11276) covalent geometry : angle 1.33369 / 0.79 (15348) SS BOND : bond 0.30545 / 17.34 ( 6) SS BOND : angle 10.61625 / 8.69 ( 12) hydrogen bonds : bond 0.19555 / 12.68 ( 612) hydrogen bonds : angle 9.29327 / 6.51 ( 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 : 0.314 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: 0.4671 time to fit residues: 100.9268 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 : 0.401 ------------------------------------------------------------------------------- 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... 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 = 0.157349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140295 restraints weight = 11777.087| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.47 r_work: 0.3446 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11282 Z= 0.185 Angle : 0.632 6.294 15360 Z= 0.333 Chirality : 0.042 0.127 1794 Planarity : 0.006 0.066 1914 Dihedral : 6.501 78.049 1512 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.18 % Allowed : 22.32 % Favored : 75.50 % 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 0.004 0.000 ARG A 276 TYR 0.017 0.002 TYR A 463 PHE 0.018 0.002 PHE B 317 TRP 0.011 0.001 TRP B 281 HIS 0.004 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (11276) covalent geometry : angle 0.63040 / 0.33 (15348) SS BOND : bond 0.00554 / 0.29 ( 6) SS BOND : angle 1.67061 / 1.48 ( 12) hydrogen bonds : bond 0.04880 / 3.24 ( 612) hydrogen bonds : angle 5.42236 / 3.83 ( 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 182 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.415 Fit side-chains REVERT: A 122 TYR cc_start: 0.8138 (m-80) cc_final: 0.7776 (m-80) REVERT: A 237 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7844 (p0) REVERT: A 365 LYS cc_start: 0.8241 (mtpp) cc_final: 0.7946 (mtmt) REVERT: A 570 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8278 (tt) REVERT: A 636 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: A 693 MET cc_start: 0.8603 (mmm) cc_final: 0.8293 (tpt) REVERT: B 122 TYR cc_start: 0.8142 (m-80) cc_final: 0.7775 (m-80) REVERT: B 237 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7851 (p0) REVERT: B 365 LYS cc_start: 0.8251 (mtpp) cc_final: 0.7961 (mtmt) REVERT: B 570 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8282 (tt) REVERT: B 636 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: B 693 MET cc_start: 0.8611 (mmm) cc_final: 0.8300 (tpt) outliers start: 26 outliers final: 12 residues processed: 172 average time/residue: 0.4335 time to fit residues: 82.1642 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 : 0.361 ------------------------------------------------------------------------------- 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: 0.0570 chunk 53 optimal weight: 0.3980 chunk 110 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3783 r_free = 0.3783 target = 0.157636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140474 restraints weight = 11753.562| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.47 r_work: 0.3454 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11282 Z= 0.156 Angle : 0.559 5.554 15360 Z= 0.291 Chirality : 0.040 0.126 1794 Planarity : 0.005 0.055 1914 Dihedral : 5.934 78.012 1508 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.02 % Allowed : 20.30 % 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: -0.79 (0.21), residues: 1392 helix: -0.09 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -1.06 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 653 TYR 0.009 0.001 TYR B 509 PHE 0.017 0.002 PHE A 459 TRP 0.010 0.001 TRP A 87 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (11276) covalent geometry : angle 0.55782 / 0.29 (15348) SS BOND : bond 0.00401 / 0.22 ( 6) SS BOND : angle 1.24273 / 1.10 ( 12) hydrogen bonds : bond 0.04405 / 2.92 ( 612) hydrogen bonds : angle 4.91020 / 3.48 ( 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 192 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.469 Fit side-chains REVERT: A 55 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: A 122 TYR cc_start: 0.8100 (m-80) cc_final: 0.7713 (m-80) REVERT: A 237 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7890 (p0) REVERT: A 365 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7832 (mtmt) REVERT: A 483 ILE cc_start: 0.8476 (mt) cc_final: 0.8274 (mt) REVERT: B 55 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: B 122 TYR cc_start: 0.8089 (m-80) cc_final: 0.7701 (m-80) REVERT: B 365 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7854 (mtmt) REVERT: B 483 ILE cc_start: 0.8464 (mt) cc_final: 0.8262 (mt) outliers start: 36 outliers final: 14 residues processed: 182 average time/residue: 0.4078 time to fit residues: 82.2181 Evaluate side-chains 156 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 303 SER Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 498 MET 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: 0.9980 chunk 83 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 128 optimal weight: 0.0970 chunk 2 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 HIS A 538 ASN B 237 ASN B 327 HIS B 538 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.156654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.139372 restraints weight = 11820.687| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.48 r_work: 0.3446 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11282 Z= 0.174 Angle : 0.561 5.497 15360 Z= 0.289 Chirality : 0.041 0.123 1794 Planarity : 0.005 0.050 1914 Dihedral : 5.796 78.953 1508 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.19 % Allowed : 20.47 % 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: -0.25 (0.22), residues: 1392 helix: 0.39 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.90 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 653 TYR 0.010 0.001 TYR B 463 PHE 0.016 0.002 PHE A 459 TRP 0.009 0.001 TRP B 87 HIS 0.002 0.001 HIS A 645 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (11276) covalent geometry : angle 0.56067 / 0.29 (15348) SS BOND : bond 0.00304 / 0.18 ( 6) SS BOND : angle 1.09031 / 0.97 ( 12) hydrogen bonds : bond 0.04377 / 2.91 ( 612) hydrogen bonds : angle 4.77856 / 3.39 ( 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 184 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.332 Fit side-chains REVERT: A 55 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7498 (mm-30) REVERT: A 122 TYR cc_start: 0.8092 (m-80) cc_final: 0.7734 (m-80) REVERT: A 237 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7876 (p0) REVERT: A 365 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7909 (mttt) REVERT: A 393 GLU cc_start: 0.7602 (tt0) cc_final: 0.6929 (pm20) REVERT: A 636 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: B 55 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: B 122 TYR cc_start: 0.8087 (m-80) cc_final: 0.7728 (m-80) REVERT: B 365 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7944 (mttt) REVERT: B 393 GLU cc_start: 0.7647 (tt0) cc_final: 0.6923 (pm20) REVERT: B 636 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7226 (tt0) outliers start: 38 outliers final: 14 residues processed: 170 average time/residue: 0.3992 time to fit residues: 74.7087 Evaluate side-chains 161 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 579 ASN 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 303 SER Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 579 ASN 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: 0.3980 chunk 115 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 117 optimal weight: 0.4980 chunk 116 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3771 r_free = 0.3771 target = 0.156318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.139148 restraints weight = 11572.233| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.45 r_work: 0.3448 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2399 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= 0.177 Angle : 0.559 5.563 15360 Z= 0.287 Chirality : 0.041 0.123 1794 Planarity : 0.005 0.047 1914 Dihedral : 5.779 80.940 1508 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.44 % Allowed : 20.55 % Favored : 76.01 % 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: 0.04 (0.22), residues: 1392 helix: 0.60 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.76 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 679 TYR 0.010 0.001 TYR A 463 PHE 0.017 0.002 PHE A 459 TRP 0.008 0.001 TRP B 87 HIS 0.002 0.001 HIS B 645 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (11276) covalent geometry : angle 0.55862 / 0.29 (15348) SS BOND : bond 0.00495 / 0.27 ( 6) SS BOND : angle 1.02798 / 0.90 ( 12) hydrogen bonds : bond 0.04357 / 2.89 ( 612) hydrogen bonds : angle 4.72943 / 3.35 ( 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 188 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.441 Fit side-chains REVERT: A 55 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: A 122 TYR cc_start: 0.8078 (m-80) cc_final: 0.7749 (m-80) REVERT: A 365 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7850 (mttt) REVERT: A 393 GLU cc_start: 0.7584 (tt0) cc_final: 0.6917 (pm20) REVERT: A 636 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: B 55 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: B 122 TYR cc_start: 0.8082 (m-80) cc_final: 0.7755 (m-80) REVERT: B 268 LEU cc_start: 0.8594 (tt) cc_final: 0.8361 (tp) REVERT: B 365 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7870 (mttt) REVERT: B 393 GLU cc_start: 0.7638 (tt0) cc_final: 0.6928 (pm20) REVERT: B 636 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7198 (tt0) outliers start: 41 outliers final: 14 residues processed: 174 average time/residue: 0.4001 time to fit residues: 77.2674 Evaluate side-chains 162 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 303 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 407 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 85 LEU 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 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: 0.7980 chunk 40 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 ASN A 327 HIS B 327 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140124 restraints weight = 11643.698| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.22 r_work: 0.3470 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2513 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= 0.198 Angle : 0.580 5.529 15360 Z= 0.297 Chirality : 0.042 0.140 1794 Planarity : 0.005 0.048 1914 Dihedral : 5.855 83.853 1508 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.03 % Allowed : 20.05 % 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: 0.02 (0.22), residues: 1392 helix: 0.60 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.81 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 239 TYR 0.012 0.001 TYR A 463 PHE 0.017 0.002 PHE B 459 TRP 0.008 0.001 TRP B 87 HIS 0.002 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (11276) covalent geometry : angle 0.57998 / 0.30 (15348) SS BOND : bond 0.00380 / 0.22 ( 6) SS BOND : angle 1.01404 / 0.89 ( 12) hydrogen bonds : bond 0.04458 / 2.96 ( 612) hydrogen bonds : angle 4.77912 / 3.40 ( 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 194 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.444 Fit side-chains REVERT: A 55 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7346 (mm-30) REVERT: A 63 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: A 103 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7762 (tp) REVERT: A 122 TYR cc_start: 0.8003 (m-80) cc_final: 0.7693 (m-80) REVERT: A 365 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7728 (mttt) REVERT: A 393 GLU cc_start: 0.7419 (tt0) cc_final: 0.6693 (pm20) REVERT: A 636 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: B 55 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7352 (mm-30) REVERT: B 63 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: B 83 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8213 (mp) REVERT: B 103 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7774 (tp) REVERT: B 122 TYR cc_start: 0.8005 (m-80) cc_final: 0.7694 (m-80) REVERT: B 365 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7727 (mttt) REVERT: B 393 GLU cc_start: 0.7454 (tt0) cc_final: 0.6712 (pm20) REVERT: B 636 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7135 (tt0) outliers start: 48 outliers final: 22 residues processed: 179 average time/residue: 0.4302 time to fit residues: 85.3100 Evaluate side-chains 173 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 85 LEU 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 626 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 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 85 LEU 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 626 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=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: 0.8980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 0.0030 chunk 139 optimal weight: 0.0670 chunk 75 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.4928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3773 r_free = 0.3773 target = 0.156717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141542 restraints weight = 11581.820| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.20 r_work: 0.3489 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11282 Z= 0.167 Angle : 0.559 5.499 15360 Z= 0.286 Chirality : 0.041 0.127 1794 Planarity : 0.004 0.047 1914 Dihedral : 5.883 87.144 1508 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.52 % Allowed : 20.47 % Favored : 76.01 % 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: 0.19 (0.22), residues: 1392 helix: 0.74 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.74 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 282 TYR 0.010 0.001 TYR A 463 PHE 0.016 0.002 PHE B 459 TRP 0.010 0.001 TRP A 275 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (11276) covalent geometry : angle 0.55861 / 0.29 (15348) SS BOND : bond 0.00330 / 0.19 ( 6) SS BOND : angle 0.89238 / 0.79 ( 12) hydrogen bonds : bond 0.04322 / 2.87 ( 612) hydrogen bonds : angle 4.68519 / 3.33 ( 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 190 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.443 Fit side-chains REVERT: A 55 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7290 (mm-30) REVERT: A 63 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: A 85 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8278 (mp) REVERT: A 103 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7774 (tp) REVERT: A 122 TYR cc_start: 0.7986 (m-80) cc_final: 0.7628 (m-80) REVERT: A 365 LYS cc_start: 0.8011 (mtpp) cc_final: 0.7684 (mttt) REVERT: A 393 GLU cc_start: 0.7423 (tt0) cc_final: 0.6737 (pm20) REVERT: A 636 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7092 (tt0) REVERT: B 55 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7285 (mm-30) REVERT: B 63 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: B 85 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8268 (mp) REVERT: B 103 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7783 (tp) REVERT: B 122 TYR cc_start: 0.7984 (m-80) cc_final: 0.7627 (m-80) REVERT: B 365 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7687 (mttt) REVERT: B 393 GLU cc_start: 0.7456 (tt0) cc_final: 0.6742 (pm20) REVERT: B 636 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7091 (tt0) outliers start: 42 outliers final: 18 residues processed: 179 average time/residue: 0.4256 time to fit residues: 83.6404 Evaluate side-chains 171 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 85 LEU 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 689 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 85 LEU 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 689 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 88 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 44 optimal weight: 0.0070 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 HIS A 694 GLN B 327 HIS B 694 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.156519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141298 restraints weight = 11665.827| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.22 r_work: 0.3492 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2651 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= 0.158 Angle : 0.555 6.288 15360 Z= 0.284 Chirality : 0.041 0.125 1794 Planarity : 0.004 0.047 1914 Dihedral : 5.896 89.328 1508 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.02 % Allowed : 21.22 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.39 (0.22), residues: 1392 helix: 0.95 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.71 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 653 TYR 0.009 0.001 TYR A 463 PHE 0.016 0.001 PHE A 459 TRP 0.009 0.001 TRP A 275 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (11276) covalent geometry : angle 0.55447 / 0.28 (15348) SS BOND : bond 0.00422 / 0.23 ( 6) SS BOND : angle 0.88848 / 0.77 ( 12) hydrogen bonds : bond 0.04294 / 2.85 ( 612) hydrogen bonds : angle 4.64666 / 3.30 ( 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 184 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.393 Fit side-chains REVERT: A 55 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: A 63 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: A 85 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8253 (mp) REVERT: A 86 LYS cc_start: 0.7885 (ptpt) cc_final: 0.7020 (mmtp) REVERT: A 103 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7772 (tp) REVERT: A 122 TYR cc_start: 0.7950 (m-80) cc_final: 0.7592 (m-80) REVERT: A 365 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7730 (mttt) REVERT: A 393 GLU cc_start: 0.7409 (tt0) cc_final: 0.6605 (mp0) REVERT: A 636 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: B 55 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: B 63 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: B 85 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8238 (mp) REVERT: B 86 LYS cc_start: 0.7870 (ptpt) cc_final: 0.6989 (mmtp) REVERT: B 103 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7781 (tp) REVERT: B 122 TYR cc_start: 0.7958 (m-80) cc_final: 0.7600 (m-80) REVERT: B 365 LYS cc_start: 0.8022 (mtpp) cc_final: 0.7735 (mttt) REVERT: B 393 GLU cc_start: 0.7442 (tt0) cc_final: 0.6619 (mp0) REVERT: B 636 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7088 (tt0) outliers start: 36 outliers final: 18 residues processed: 174 average time/residue: 0.4245 time to fit residues: 82.0749 Evaluate side-chains 172 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 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 85 LEU 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 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 85 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 41 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 120 optimal weight: 0.0040 chunk 48 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 HIS A 694 GLN B 327 HIS B 694 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141139 restraints weight = 11668.571| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.22 r_work: 0.3489 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11282 Z= 0.162 Angle : 0.561 6.528 15360 Z= 0.285 Chirality : 0.041 0.125 1794 Planarity : 0.004 0.045 1914 Dihedral : 5.890 88.653 1508 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.02 % Allowed : 21.06 % 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: 0.47 (0.22), residues: 1392 helix: 1.01 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.67 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 230 TYR 0.010 0.001 TYR A 463 PHE 0.016 0.002 PHE B 459 TRP 0.009 0.001 TRP A 275 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (11276) covalent geometry : angle 0.56032 / 0.29 (15348) SS BOND : bond 0.00404 / 0.23 ( 6) SS BOND : angle 0.89514 / 0.77 ( 12) hydrogen bonds : bond 0.04284 / 2.84 ( 612) hydrogen bonds : angle 4.63599 / 3.30 ( 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 185 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.262 Fit side-chains REVERT: A 55 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7273 (mm-30) REVERT: A 63 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: A 85 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8254 (mp) REVERT: A 86 LYS cc_start: 0.7828 (ptpt) cc_final: 0.7031 (mmtp) REVERT: A 103 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7767 (tp) REVERT: A 122 TYR cc_start: 0.7945 (m-80) cc_final: 0.7596 (m-80) REVERT: A 365 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7726 (mttt) REVERT: A 393 GLU cc_start: 0.7375 (tt0) cc_final: 0.6650 (pm20) REVERT: A 636 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: B 55 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: B 63 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: B 85 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8243 (mp) REVERT: B 86 LYS cc_start: 0.7805 (ptpt) cc_final: 0.6996 (mmtp) REVERT: B 103 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7773 (tp) REVERT: B 122 TYR cc_start: 0.7948 (m-80) cc_final: 0.7598 (m-80) REVERT: B 365 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7730 (mttt) REVERT: B 393 GLU cc_start: 0.7414 (tt0) cc_final: 0.6663 (pm20) REVERT: B 636 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7081 (tt0) outliers start: 36 outliers final: 18 residues processed: 173 average time/residue: 0.4031 time to fit residues: 77.0656 Evaluate side-chains 174 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 85 LEU 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 689 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 85 LEU 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 689 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 79 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 139 optimal weight: 0.7980 chunk 86 optimal weight: 0.0050 chunk 37 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 HIS A 694 GLN B 327 HIS B 694 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141618 restraints weight = 11649.405| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.22 r_work: 0.3488 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11282 Z= 0.157 Angle : 0.560 7.044 15360 Z= 0.284 Chirality : 0.041 0.125 1794 Planarity : 0.004 0.044 1914 Dihedral : 5.851 86.659 1508 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.02 % Allowed : 21.31 % 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: 0.55 (0.22), residues: 1392 helix: 1.06 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.62 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 230 TYR 0.009 0.001 TYR A 490 PHE 0.015 0.001 PHE A 459 TRP 0.011 0.001 TRP A 275 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (11276) covalent geometry : angle 0.55941 / 0.28 (15348) SS BOND : bond 0.00286 / 0.17 ( 6) SS BOND : angle 0.86606 / 0.74 ( 12) hydrogen bonds : bond 0.04252 / 2.82 ( 612) hydrogen bonds : angle 4.61152 / 3.28 ( 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 179 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.329 Fit side-chains REVERT: A 55 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7255 (mm-30) REVERT: A 63 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: A 86 LYS cc_start: 0.7772 (ptpt) cc_final: 0.7006 (mmtp) REVERT: A 103 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7754 (tp) REVERT: A 109 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7337 (mp0) REVERT: A 122 TYR cc_start: 0.7930 (m-80) cc_final: 0.7602 (m-80) REVERT: A 365 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7718 (mttt) REVERT: A 393 GLU cc_start: 0.7368 (tt0) cc_final: 0.6593 (pm20) REVERT: A 636 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: A 693 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7115 (tpp) REVERT: B 55 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: B 63 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: B 85 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8232 (mp) REVERT: B 86 LYS cc_start: 0.7792 (ptpt) cc_final: 0.7012 (mmtp) REVERT: B 103 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7759 (tp) REVERT: B 109 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7337 (mp0) REVERT: B 122 TYR cc_start: 0.7931 (m-80) cc_final: 0.7605 (m-80) REVERT: B 365 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7721 (mttt) REVERT: B 393 GLU cc_start: 0.7401 (tt0) cc_final: 0.6596 (pm20) REVERT: B 636 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: B 693 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.7113 (tpp) outliers start: 36 outliers final: 18 residues processed: 171 average time/residue: 0.4166 time to fit residues: 78.8208 Evaluate side-chains 173 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 689 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 85 LEU 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 689 THR Chi-restraints excluded: chain B residue 693 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 36 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 111 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 122 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3782 r_free = 0.3782 target = 0.157897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141672 restraints weight = 11695.344| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.34 r_work: 0.3532 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11282 Z= 0.143 Angle : 0.547 7.733 15360 Z= 0.278 Chirality : 0.040 0.123 1794 Planarity : 0.004 0.044 1914 Dihedral : 5.793 85.032 1508 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.43 % Allowed : 21.06 % 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: 0.67 (0.22), residues: 1392 helix: 1.15 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.55 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 653 TYR 0.010 0.001 TYR A 490 PHE 0.015 0.001 PHE B 459 TRP 0.011 0.001 TRP A 275 HIS 0.002 0.001 HIS B 645 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (11276) covalent geometry : angle 0.54705 / 0.28 (15348) SS BOND : bond 0.00288 / 0.17 ( 6) SS BOND : angle 0.81535 / 0.71 ( 12) hydrogen bonds : bond 0.04183 / 2.78 ( 612) hydrogen bonds : angle 4.56168 / 3.24 ( 1794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3026.08 seconds wall clock time: 52 minutes 36.36 seconds (3156.36 seconds total)