Starting phenix.real_space_refine on Tue Jul 29 08:02:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xa9_33088/07_2025/7xa9_33088.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xa9_33088/07_2025/7xa9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xa9_33088/07_2025/7xa9_33088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xa9_33088/07_2025/7xa9_33088.map" model { file = "/net/cci-nas-00/data/ceres_data/7xa9_33088/07_2025/7xa9_33088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xa9_33088/07_2025/7xa9_33088.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 13.56, per 1000 atoms: 1.23 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: 2.45 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.30 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: 3.47 Time building geometry restraints manager: 2.92 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: 0.05 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: 69.220 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 33.920 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.970 ------------------------------------------------------------------------------- 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 : 6.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.003 TRP A 274 HIS 0.013 0.002 HIS A 208 PHE 0.035 0.004 PHE A 317 TYR 0.031 0.003 TYR A 490 ARG 0.003 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.19555 ( 612) hydrogen bonds : angle 9.29327 ( 1794) SS BOND : bond 0.30545 ( 6) SS BOND : angle 10.61625 ( 12) covalent geometry : bond 0.01037 (11276) covalent geometry : angle 1.33369 (15348) *********************** 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 : 1.218 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: 0.8417 (tp) REVERT: A 276 ARG cc_start: 0.8301 (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: 0.7430 (m-80) REVERT: B 268 LEU cc_start: 0.8650 (tt) cc_final: 0.8417 (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: 1.1424 time to fit residues: 246.7613 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 : 1.212 ------------------------------------------------------------------------------- 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 118 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.157042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140042 restraints weight = 11727.995| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.46 r_work: 0.3445 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11282 Z= 0.187 Angle : 0.629 6.011 15360 Z= 0.332 Chirality : 0.042 0.134 1794 Planarity : 0.006 0.062 1914 Dihedral : 9.482 84.322 1574 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.18 % Allowed : 21.98 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.20), residues: 1392 helix: -1.22 (0.16), residues: 826 sheet: None (None), residues: 0 loop : -1.34 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 87 HIS 0.005 0.001 HIS A 53 PHE 0.017 0.002 PHE B 317 TYR 0.018 0.002 TYR A 463 ARG 0.004 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.04815 ( 612) hydrogen bonds : angle 5.43322 ( 1794) SS BOND : bond 0.00281 ( 6) SS BOND : angle 1.56077 ( 12) covalent geometry : bond 0.00430 (11276) covalent geometry : angle 0.62802 (15348) *********************** 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 188 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 1.764 Fit side-chains REVERT: A 122 TYR cc_start: 0.8136 (m-80) cc_final: 0.7774 (m-80) REVERT: A 237 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7878 (p0) REVERT: A 365 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7944 (mtmt) REVERT: A 483 ILE cc_start: 0.8502 (mt) cc_final: 0.8296 (mt) REVERT: A 570 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8289 (tt) REVERT: A 636 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: B 122 TYR cc_start: 0.8136 (m-80) cc_final: 0.7770 (m-80) REVERT: B 237 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7884 (p0) REVERT: B 365 LYS cc_start: 0.8235 (mtpp) cc_final: 0.7954 (mtmt) REVERT: B 483 ILE cc_start: 0.8494 (mt) cc_final: 0.8290 (mt) REVERT: B 570 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8287 (tt) REVERT: B 636 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7207 (tt0) outliers start: 26 outliers final: 12 residues processed: 176 average time/residue: 1.4069 time to fit residues: 270.9444 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 : 1.119 ------------------------------------------------------------------------------- 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 116 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 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 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 = 0.3753 r_free = 0.3753 target = 0.154753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137409 restraints weight = 11788.641| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.47 r_work: 0.3430 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11282 Z= 0.204 Angle : 0.604 5.950 15360 Z= 0.313 Chirality : 0.042 0.127 1794 Planarity : 0.005 0.051 1914 Dihedral : 8.431 72.976 1570 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.52 % Allowed : 19.30 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1392 helix: -0.18 (0.17), residues: 836 sheet: None (None), residues: 0 loop : -0.93 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 87 HIS 0.002 0.001 HIS A 645 PHE 0.018 0.002 PHE A 459 TYR 0.013 0.002 TYR A 463 ARG 0.003 0.000 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 612) hydrogen bonds : angle 5.04625 ( 1794) SS BOND : bond 0.00331 ( 6) SS BOND : angle 1.32386 ( 12) covalent geometry : bond 0.00481 (11276) covalent geometry : angle 0.60287 (15348) *********************** 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: 42 poor density : 150 time to evaluate : 1.588 Fit side-chains REVERT: A 55 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: A 122 TYR cc_start: 0.8131 (m-80) cc_final: 0.7753 (m-80) REVERT: A 237 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7840 (p0) REVERT: A 365 LYS cc_start: 0.8247 (mtpp) cc_final: 0.7908 (mtmt) REVERT: A 393 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: A 483 ILE cc_start: 0.8484 (mt) cc_final: 0.8281 (mt) REVERT: B 55 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: B 122 TYR cc_start: 0.8130 (m-80) cc_final: 0.7750 (m-80) REVERT: B 237 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7826 (p0) REVERT: B 365 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7920 (mtmt) REVERT: B 393 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: B 483 ILE cc_start: 0.8481 (mt) cc_final: 0.8279 (mt) outliers start: 42 outliers final: 18 residues processed: 178 average time/residue: 1.2552 time to fit residues: 246.0749 Evaluate side-chains 166 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.220 ------------------------------------------------------------------------------- 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 393 GLU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 626 LEU 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 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 393 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.153733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138209 restraints weight = 11694.323| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.22 r_work: 0.3453 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11282 Z= 0.239 Angle : 0.619 5.828 15360 Z= 0.317 Chirality : 0.043 0.132 1794 Planarity : 0.005 0.047 1914 Dihedral : 8.328 74.605 1570 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.86 % Allowed : 19.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.22), residues: 1392 helix: 0.16 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -0.80 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 87 HIS 0.004 0.001 HIS A 327 PHE 0.018 0.002 PHE B 459 TYR 0.013 0.002 TYR A 463 ARG 0.003 0.000 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 612) hydrogen bonds : angle 5.01237 ( 1794) SS BOND : bond 0.00442 ( 6) SS BOND : angle 1.31872 ( 12) covalent geometry : bond 0.00572 (11276) covalent geometry : angle 0.61775 (15348) *********************** 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 182 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 1.253 Fit side-chains REVERT: A 55 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: A 85 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8352 (mp) REVERT: A 122 TYR cc_start: 0.8055 (m-80) cc_final: 0.7693 (m-80) REVERT: A 237 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7675 (p0) REVERT: A 365 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7832 (mttt) REVERT: A 393 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6800 (pm20) REVERT: A 636 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: B 55 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: B 85 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8352 (mp) REVERT: B 122 TYR cc_start: 0.8055 (m-80) cc_final: 0.7692 (m-80) REVERT: B 237 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7662 (p0) REVERT: B 365 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7837 (mttt) REVERT: B 393 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6795 (pm20) REVERT: B 636 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7147 (tt0) outliers start: 46 outliers final: 12 residues processed: 166 average time/residue: 0.9578 time to fit residues: 175.3101 Evaluate side-chains 146 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 393 GLU 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 393 GLU 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 26 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 59 optimal weight: 0.0670 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.155812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138606 restraints weight = 11640.186| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.47 r_work: 0.3430 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2454 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= 0.161 Angle : 0.553 5.797 15360 Z= 0.285 Chirality : 0.041 0.120 1794 Planarity : 0.004 0.047 1914 Dihedral : 7.705 74.722 1570 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.03 % Allowed : 18.79 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1392 helix: 0.51 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.84 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.002 0.001 HIS A 327 PHE 0.017 0.002 PHE A 459 TYR 0.009 0.001 TYR A 490 ARG 0.003 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 612) hydrogen bonds : angle 4.74542 ( 1794) SS BOND : bond 0.00270 ( 6) SS BOND : angle 0.95886 ( 12) covalent geometry : bond 0.00373 (11276) covalent geometry : angle 0.55208 (15348) *********************** 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 192 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 1.141 Fit side-chains REVERT: A 55 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7431 (mm-30) REVERT: A 63 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: A 83 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8297 (mp) REVERT: A 122 TYR cc_start: 0.8087 (m-80) cc_final: 0.7714 (m-80) REVERT: A 237 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7873 (p0) REVERT: A 365 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7859 (mttt) REVERT: A 393 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6844 (pm20) REVERT: A 636 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: B 55 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: B 63 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: B 83 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8311 (mp) REVERT: B 122 TYR cc_start: 0.8091 (m-80) cc_final: 0.7718 (m-80) REVERT: B 237 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7863 (p0) REVERT: B 365 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7869 (mttt) REVERT: B 393 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6844 (pm20) REVERT: B 636 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7209 (tt0) outliers start: 48 outliers final: 16 residues processed: 178 average time/residue: 1.0171 time to fit residues: 200.2749 Evaluate side-chains 162 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 151 VAL Chi-restraints excluded: chain A residue 237 ASN 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 393 GLU 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 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 151 VAL Chi-restraints excluded: chain B residue 237 ASN 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 393 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 116 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 54 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 132 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 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 408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.139501 restraints weight = 11636.437| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.48 r_work: 0.3527 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2542 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= 0.152 Angle : 0.546 6.154 15360 Z= 0.281 Chirality : 0.040 0.121 1794 Planarity : 0.004 0.046 1914 Dihedral : 7.442 75.598 1570 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.61 % Allowed : 19.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1392 helix: 0.76 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.74 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 87 HIS 0.005 0.001 HIS A 327 PHE 0.016 0.001 PHE B 459 TYR 0.010 0.001 TYR B 490 ARG 0.002 0.000 ARG B 653 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 612) hydrogen bonds : angle 4.65825 ( 1794) SS BOND : bond 0.00349 ( 6) SS BOND : angle 0.88676 ( 12) covalent geometry : bond 0.00352 (11276) covalent geometry : angle 0.54573 (15348) *********************** 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 185 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 1.146 Fit side-chains REVERT: A 55 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7472 (mm-30) REVERT: A 63 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: A 86 LYS cc_start: 0.8149 (ptpt) cc_final: 0.7420 (mmtp) REVERT: A 103 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7901 (tp) REVERT: A 122 TYR cc_start: 0.8056 (m-80) cc_final: 0.7702 (m-80) REVERT: A 365 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7823 (mttt) REVERT: A 393 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: A 636 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: B 55 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7464 (mm-30) REVERT: B 63 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: B 86 LYS cc_start: 0.8146 (ptpt) cc_final: 0.7416 (mmtp) REVERT: B 103 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7910 (tp) REVERT: B 122 TYR cc_start: 0.8042 (m-80) cc_final: 0.7689 (m-80) REVERT: B 365 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7840 (mttt) REVERT: B 393 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: B 636 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: B 685 ASP cc_start: 0.6129 (OUTLIER) cc_final: 0.5926 (p0) outliers start: 43 outliers final: 20 residues processed: 175 average time/residue: 0.9406 time to fit residues: 182.2400 Evaluate side-chains 165 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 393 GLU 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 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 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 393 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 111 optimal weight: 0.2980 chunk 53 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 54 optimal weight: 0.0030 overall best weight: 0.3390 ------------------------------------------------------------------------------- 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 A 408 ASN B 237 ASN B 327 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142284 restraints weight = 11813.757| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.24 r_work: 0.3499 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.003 0.035 11282 Z= 0.140 Angle : 0.530 5.320 15360 Z= 0.274 Chirality : 0.040 0.128 1794 Planarity : 0.004 0.046 1914 Dihedral : 7.244 75.631 1570 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.44 % Allowed : 20.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1392 helix: 0.91 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.68 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 87 HIS 0.004 0.001 HIS B 327 PHE 0.015 0.001 PHE A 459 TYR 0.010 0.001 TYR A 490 ARG 0.003 0.000 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 612) hydrogen bonds : angle 4.59305 ( 1794) SS BOND : bond 0.00252 ( 6) SS BOND : angle 0.80724 ( 12) covalent geometry : bond 0.00323 (11276) covalent geometry : angle 0.52972 (15348) *********************** 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 183 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 1.782 Fit side-chains REVERT: A 55 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7269 (mm-30) REVERT: A 63 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: A 86 LYS cc_start: 0.7868 (ptpt) cc_final: 0.7039 (mmtp) REVERT: A 103 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7745 (tp) REVERT: A 122 TYR cc_start: 0.7954 (m-80) cc_final: 0.7606 (m-80) REVERT: A 365 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7641 (mttt) REVERT: A 393 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6725 (pm20) REVERT: A 636 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: B 55 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7276 (mm-30) REVERT: B 63 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: B 86 LYS cc_start: 0.7858 (ptpt) cc_final: 0.7034 (mmtp) REVERT: B 103 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7759 (tp) REVERT: B 122 TYR cc_start: 0.7949 (m-80) cc_final: 0.7598 (m-80) REVERT: B 365 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7637 (mttt) REVERT: B 393 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6726 (pm20) REVERT: B 636 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7083 (tt0) outliers start: 41 outliers final: 18 residues processed: 169 average time/residue: 1.1158 time to fit residues: 209.3589 Evaluate side-chains 166 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 393 GLU 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 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 393 GLU 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 689 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 84 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 105 optimal weight: 0.5980 chunk 139 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.155920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140447 restraints weight = 11682.557| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.23 r_work: 0.3471 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2634 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= 0.182 Angle : 0.568 5.076 15360 Z= 0.292 Chirality : 0.042 0.134 1794 Planarity : 0.004 0.045 1914 Dihedral : 7.365 75.402 1570 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1392 helix: 0.87 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.66 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 87 HIS 0.003 0.001 HIS B 327 PHE 0.016 0.002 PHE A 459 TYR 0.011 0.001 TYR A 463 ARG 0.002 0.000 ARG A 492 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 612) hydrogen bonds : angle 4.69075 ( 1794) SS BOND : bond 0.00379 ( 6) SS BOND : angle 0.91412 ( 12) covalent geometry : bond 0.00433 (11276) covalent geometry : angle 0.56728 (15348) *********************** 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 183 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.240 Fit side-chains REVERT: A 55 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: A 63 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8326 (mt-10) REVERT: A 86 LYS cc_start: 0.8072 (ptpt) cc_final: 0.7431 (mmtp) REVERT: A 103 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7868 (tp) REVERT: A 122 TYR cc_start: 0.8036 (m-80) cc_final: 0.7704 (m-80) REVERT: A 365 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7849 (mttt) REVERT: A 393 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: A 685 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.5956 (p0) REVERT: B 55 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7438 (mm-30) REVERT: B 63 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8333 (mt-10) REVERT: B 86 LYS cc_start: 0.8050 (ptpt) cc_final: 0.7408 (mmtp) REVERT: B 103 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7883 (tp) REVERT: B 122 TYR cc_start: 0.8031 (m-80) cc_final: 0.7699 (m-80) REVERT: B 365 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7852 (mttt) REVERT: B 393 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: B 685 ASP cc_start: 0.6156 (OUTLIER) cc_final: 0.5948 (p0) outliers start: 38 outliers final: 16 residues processed: 171 average time/residue: 1.0069 time to fit residues: 189.4737 Evaluate side-chains 171 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 393 GLU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 588 THR 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 393 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 588 THR 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 118 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 111 optimal weight: 0.2980 chunk 67 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.156335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140933 restraints weight = 11690.031| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.23 r_work: 0.3475 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2689 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= 0.171 Angle : 0.570 6.169 15360 Z= 0.290 Chirality : 0.042 0.127 1794 Planarity : 0.004 0.044 1914 Dihedral : 7.324 75.413 1570 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.60 % Allowed : 20.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1392 helix: 1.02 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.60 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 87 HIS 0.004 0.001 HIS A 327 PHE 0.016 0.002 PHE B 459 TYR 0.011 0.001 TYR A 463 ARG 0.002 0.000 ARG A 492 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 612) hydrogen bonds : angle 4.67082 ( 1794) SS BOND : bond 0.00257 ( 6) SS BOND : angle 0.86481 ( 12) covalent geometry : bond 0.00406 (11276) covalent geometry : angle 0.56979 (15348) *********************** 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: 31 poor density : 148 time to evaluate : 1.254 Fit side-chains REVERT: A 55 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7425 (mm-30) REVERT: A 63 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: A 86 LYS cc_start: 0.8051 (ptpt) cc_final: 0.7462 (mmtp) REVERT: A 103 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7878 (tp) REVERT: A 122 TYR cc_start: 0.8014 (m-80) cc_final: 0.7704 (m-80) REVERT: A 276 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7920 (mtm-85) REVERT: A 365 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7849 (mttt) REVERT: A 393 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: B 55 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7430 (mm-30) REVERT: B 63 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8291 (mt-10) REVERT: B 86 LYS cc_start: 0.8024 (ptpt) cc_final: 0.7446 (mmtp) REVERT: B 103 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7892 (tp) REVERT: B 122 TYR cc_start: 0.8006 (m-80) cc_final: 0.7692 (m-80) REVERT: B 276 ARG cc_start: 0.8134 (mtm-85) cc_final: 0.7933 (mtm-85) REVERT: B 365 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7852 (mttt) REVERT: B 393 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6967 (pm20) outliers start: 31 outliers final: 18 residues processed: 170 average time/residue: 1.0767 time to fit residues: 200.7704 Evaluate side-chains 172 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 393 GLU 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 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 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 393 GLU 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 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 86 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 101 optimal weight: 0.0870 chunk 88 optimal weight: 0.0470 chunk 26 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.158811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143505 restraints weight = 11602.786| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.23 r_work: 0.3508 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11282 Z= 0.131 Angle : 0.536 6.443 15360 Z= 0.274 Chirality : 0.040 0.124 1794 Planarity : 0.004 0.044 1914 Dihedral : 7.024 75.209 1570 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.85 % Allowed : 21.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1392 helix: 1.20 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.49 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 275 HIS 0.002 0.001 HIS B 327 PHE 0.014 0.001 PHE B 459 TYR 0.010 0.001 TYR A 490 ARG 0.003 0.000 ARG B 653 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 612) hydrogen bonds : angle 4.51774 ( 1794) SS BOND : bond 0.00360 ( 6) SS BOND : angle 0.71260 ( 12) covalent geometry : bond 0.00300 (11276) covalent geometry : angle 0.53544 (15348) ********************** 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 176 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.275 Fit side-chains REVERT: A 55 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: A 63 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: A 86 LYS cc_start: 0.7930 (ptpt) cc_final: 0.7372 (mmtp) REVERT: A 103 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7859 (tp) REVERT: A 122 TYR cc_start: 0.8006 (m-80) cc_final: 0.7731 (m-80) REVERT: A 276 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7793 (ptt-90) REVERT: A 365 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7716 (mttt) REVERT: A 393 GLU cc_start: 0.7476 (tt0) cc_final: 0.6836 (pm20) REVERT: B 55 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: B 63 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8316 (mt-10) REVERT: B 86 LYS cc_start: 0.7917 (ptpt) cc_final: 0.7365 (mmtp) REVERT: B 103 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7873 (tp) REVERT: B 122 TYR cc_start: 0.7996 (m-80) cc_final: 0.7718 (m-80) REVERT: B 276 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7806 (ptt-90) REVERT: B 365 LYS cc_start: 0.7931 (mtpp) cc_final: 0.7714 (mttt) REVERT: B 393 GLU cc_start: 0.7527 (tt0) cc_final: 0.6826 (pm20) outliers start: 22 outliers final: 16 residues processed: 172 average time/residue: 1.2361 time to fit residues: 235.5242 Evaluate side-chains 174 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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 498 MET Chi-restraints excluded: chain A residue 579 ASN 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 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 498 MET Chi-restraints excluded: chain B residue 579 ASN 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 68 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.1980 chunk 134 optimal weight: 0.1980 chunk 66 optimal weight: 0.0970 chunk 138 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.157363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141950 restraints weight = 11687.223| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.24 r_work: 0.3496 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2774 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= 0.152 Angle : 0.559 7.363 15360 Z= 0.283 Chirality : 0.041 0.125 1794 Planarity : 0.004 0.045 1914 Dihedral : 7.092 75.029 1570 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.10 % Allowed : 21.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1392 helix: 1.18 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.45 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 275 HIS 0.002 0.001 HIS A 645 PHE 0.015 0.001 PHE B 459 TYR 0.010 0.001 TYR A 463 ARG 0.002 0.000 ARG B 653 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 612) hydrogen bonds : angle 4.57165 ( 1794) SS BOND : bond 0.00281 ( 6) SS BOND : angle 0.78164 ( 12) covalent geometry : bond 0.00355 (11276) covalent geometry : angle 0.55902 (15348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7828.62 seconds wall clock time: 142 minutes 58.01 seconds (8578.01 seconds total)