Starting phenix.real_space_refine on Wed Jun 18 19:05:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgj_36236/06_2025/8jgj_36236_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgj_36236/06_2025/8jgj_36236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jgj_36236/06_2025/8jgj_36236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgj_36236/06_2025/8jgj_36236.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgj_36236/06_2025/8jgj_36236_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgj_36236/06_2025/8jgj_36236_trim.cif" } resolution = 3.3 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= 0.002 sd= 0.033 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 S 72 5.16 5 Cl 6 4.86 5 C 7060 2.51 5 N 1780 2.21 5 O 1894 1.98 5 H 10850 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21668 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 10798 Classifications: {'peptide': 684} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 655} Chain breaks: 4 Chain: "B" Number of atoms: 10798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 10798 Classifications: {'peptide': 684} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 655} Chain breaks: 4 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 10.95, per 1000 atoms: 0.51 Number of scatterers: 21668 At special positions: 0 Unit cell: (90.21, 119.97, 109.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 6 17.00 S 72 16.00 P 6 15.00 O 1894 8.00 N 1780 7.00 C 7060 6.00 H 10850 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 161 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 562 " - pdb=" SG CYS B 568 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.45 Conformation dependent library (CDL) restraints added in 2.1 seconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 6 sheets defined 68.1% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 92 through 112 removed outlier: 3.855A pdb=" N LYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 157 removed outlier: 4.521A pdb=" N GLY A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TRP A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 203 through 233 Processing helix chain 'A' and resid 234 through 237 removed outlier: 3.787A pdb=" N CYS A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 254 through 257 removed outlier: 4.191A pdb=" N LEU A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 257' Processing helix chain 'A' and resid 258 through 274 Processing helix chain 'A' and resid 283 through 298 removed outlier: 4.201A pdb=" N HIS A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.538A pdb=" N THR A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 327 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 347 through 366 removed outlier: 3.993A pdb=" N ARG A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 391 through 420 removed outlier: 3.673A pdb=" N GLY A 397 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 426 through 443 removed outlier: 3.501A pdb=" N PHE A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.749A pdb=" N ASP A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 516 removed outlier: 3.718A pdb=" N TYR A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 505 " --> pdb=" O TRP A 501 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 552 Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.998A pdb=" N GLU A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 Processing helix chain 'A' and resid 590 through 601 removed outlier: 3.683A pdb=" N VAL A 594 " --> pdb=" O THR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 622 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 653 through 658 removed outlier: 3.909A pdb=" N VAL A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 767 through 779 removed outlier: 4.003A pdb=" N VAL A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 removed outlier: 4.085A pdb=" N LEU A 801 " --> pdb=" O LYS A 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 112 removed outlier: 3.833A pdb=" N LYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 157 removed outlier: 4.510A pdb=" N GLY B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TRP B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 203 through 233 Processing helix chain 'B' and resid 234 through 237 removed outlier: 3.786A pdb=" N CYS B 237 " --> pdb=" O PRO B 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 237' Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 254 through 257 removed outlier: 4.184A pdb=" N LEU B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 257' Processing helix chain 'B' and resid 258 through 274 Processing helix chain 'B' and resid 283 through 298 removed outlier: 4.235A pdb=" N HIS B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.551A pdb=" N THR B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 327 Processing helix chain 'B' and resid 328 through 339 Processing helix chain 'B' and resid 347 through 366 removed outlier: 3.983A pdb=" N ARG B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 391 through 420 removed outlier: 3.963A pdb=" N ILE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 426 through 443 removed outlier: 3.522A pdb=" N PHE B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 469 through 473 removed outlier: 3.844A pdb=" N ASP B 473 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 516 removed outlier: 3.536A pdb=" N TYR B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 505 " --> pdb=" O TRP B 501 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.956A pdb=" N GLU B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 588 Processing helix chain 'B' and resid 590 through 601 removed outlier: 3.737A pdb=" N VAL B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 622 Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 653 through 658 removed outlier: 3.932A pdb=" N VAL B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 709 through 722 Processing helix chain 'B' and resid 767 through 779 removed outlier: 3.983A pdb=" N VAL B 771 " --> pdb=" O PRO B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 805 removed outlier: 4.080A pdb=" N LEU B 801 " --> pdb=" O LYS B 797 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 691 through 695 removed outlier: 6.544A pdb=" N PHE A 692 " --> pdb=" O PHE A 706 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE A 706 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 694 " --> pdb=" O VAL A 704 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 782 through 786 Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA5, first strand: chain 'B' and resid 691 through 695 Processing sheet with id=AA6, first strand: chain 'B' and resid 782 through 786 645 hydrogen bonds defined for protein. 1908 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: 8.43 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 10826 1.02 - 1.22: 31 1.22 - 1.42: 4608 1.42 - 1.61: 6367 1.61 - 1.81: 108 Bond restraints: 21940 Sorted by residual: bond pdb=" NZ LYS B 281 " pdb=" HZ3 LYS B 281 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" NZ LYS B 245 " pdb=" HZ3 LYS B 245 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" NZ LYS A 281 " pdb=" HZ3 LYS A 281 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" NZ LYS A 281 " pdb=" HZ2 LYS A 281 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" NZ LYS B 281 " pdb=" HZ1 LYS B 281 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 21935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 39063 1.54 - 3.08: 518 3.08 - 4.63: 59 4.63 - 6.17: 10 6.17 - 7.71: 8 Bond angle restraints: 39658 Sorted by residual: angle pdb=" N GLU B 339 " pdb=" CA GLU B 339 " pdb=" C GLU B 339 " ideal model delta sigma weight residual 112.45 120.02 -7.57 1.39e+00 5.18e-01 2.96e+01 angle pdb=" N GLU A 339 " pdb=" CA GLU A 339 " pdb=" C GLU A 339 " ideal model delta sigma weight residual 112.04 119.75 -7.71 1.44e+00 4.82e-01 2.87e+01 angle pdb=" N GLU A 282 " pdb=" CA GLU A 282 " pdb=" C GLU A 282 " ideal model delta sigma weight residual 112.45 105.31 7.14 1.39e+00 5.18e-01 2.64e+01 angle pdb=" N GLU B 282 " pdb=" CA GLU B 282 " pdb=" C GLU B 282 " ideal model delta sigma weight residual 112.45 105.65 6.80 1.39e+00 5.18e-01 2.39e+01 angle pdb=" C GLU A 339 " pdb=" CA GLU A 339 " pdb=" CB GLU A 339 " ideal model delta sigma weight residual 110.56 104.31 6.25 1.83e+00 2.99e-01 1.16e+01 ... (remaining 39653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 9196 16.94 - 33.87: 789 33.87 - 50.81: 227 50.81 - 67.75: 118 67.75 - 84.69: 20 Dihedral angle restraints: 10350 sinusoidal: 5518 harmonic: 4832 Sorted by residual: dihedral pdb=" CA ILE A 253 " pdb=" C ILE A 253 " pdb=" N ARG A 254 " pdb=" CA ARG A 254 " ideal model delta harmonic sigma weight residual -180.00 -161.59 -18.41 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ILE B 253 " pdb=" C ILE B 253 " pdb=" N ARG B 254 " pdb=" CA ARG B 254 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CB GLU B 599 " pdb=" CG GLU B 599 " pdb=" CD GLU B 599 " pdb=" OE1 GLU B 599 " ideal model delta sinusoidal sigma weight residual 0.00 -84.69 84.69 1 3.00e+01 1.11e-03 9.68e+00 ... (remaining 10347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1509 0.061 - 0.121: 174 0.121 - 0.182: 9 0.182 - 0.242: 2 0.242 - 0.303: 4 Chirality restraints: 1698 Sorted by residual: chirality pdb=" C2' ATP B 901 " pdb=" C1' ATP B 901 " pdb=" C3' ATP B 901 " pdb=" O2' ATP B 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C2' ATP A 901 " pdb=" C1' ATP A 901 " pdb=" C3' ATP A 901 " pdb=" O2' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' ATP B 901 " pdb=" C2' ATP B 901 " pdb=" C4' ATP B 901 " pdb=" O3' ATP B 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1695 not shown) Planarity restraints: 3144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 283 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A 284 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 283 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO B 284 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 245 " -0.010 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" N THR A 246 " 0.032 2.00e-02 2.50e+03 pdb=" CA THR A 246 " -0.008 2.00e-02 2.50e+03 pdb=" H THR A 246 " -0.014 2.00e-02 2.50e+03 ... (remaining 3141 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1923 2.22 - 2.81: 47095 2.81 - 3.41: 61251 3.41 - 4.00: 79424 4.00 - 4.60: 124746 Nonbonded interactions: 314439 Sorted by model distance: nonbonded pdb=" O MET A 683 " pdb=" HG1 THR A 687 " model vdw 1.623 2.450 nonbonded pdb=" O PHE A 443 " pdb="HH11 ARG A 449 " model vdw 1.625 2.450 nonbonded pdb=" O PHE B 518 " pdb=" HG SER B 524 " model vdw 1.640 2.450 nonbonded pdb=" O PHE A 518 " pdb=" HG SER A 524 " model vdw 1.644 2.450 nonbonded pdb=" HZ3 LYS A 798 " pdb=" O3G ATP A 901 " model vdw 1.651 2.450 ... (remaining 314434 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: 0.07 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: 1.230 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: 0.420 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.190 Process input model: 50.480 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.009 0.892 11097 Z= 0.866 Angle : 0.558 7.711 15078 Z= 0.308 Chirality : 0.040 0.303 1698 Planarity : 0.004 0.052 1844 Dihedral : 14.575 84.686 3966 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.23 (0.23), residues: 1348 helix: 0.95 (0.18), residues: 830 sheet: -2.07 (1.04), residues: 30 loop : -1.03 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 403 HIS 0.003 0.001 HIS B 553 PHE 0.014 0.001 PHE A 300 TYR 0.017 0.001 TYR A 211 ARG 0.004 0.000 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.13708 ( 645) hydrogen bonds : angle 6.77670 ( 1908) SS BOND : bond 0.00227 ( 6) SS BOND : angle 0.45043 ( 12) covalent geometry : bond 0.00357 (11090) covalent geometry : angle 0.55817 (15066) Misc. bond : bond 0.89152 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 MET cc_start: 0.7682 (ppp) cc_final: 0.7279 (ptt) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.5475 time to fit residues: 119.9595 Evaluate side-chains 130 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 106 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.191504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.150546 restraints weight = 34294.814| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.05 r_work: 0.3578 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11097 Z= 0.168 Angle : 0.522 5.760 15078 Z= 0.276 Chirality : 0.038 0.143 1698 Planarity : 0.004 0.052 1844 Dihedral : 8.674 80.063 1544 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.23 % Allowed : 5.99 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.53 (0.23), residues: 1348 helix: 1.27 (0.18), residues: 842 sheet: -2.11 (1.01), residues: 30 loop : -1.13 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 403 HIS 0.003 0.001 HIS B 787 PHE 0.011 0.001 PHE B 377 TYR 0.017 0.001 TYR A 211 ARG 0.003 0.000 ARG A 776 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 645) hydrogen bonds : angle 5.02542 ( 1908) SS BOND : bond 0.00273 ( 6) SS BOND : angle 0.47784 ( 12) covalent geometry : bond 0.00386 (11090) covalent geometry : angle 0.52207 (15066) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 149 average time/residue: 0.5366 time to fit residues: 114.0880 Evaluate side-chains 145 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 774 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 123 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 124 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.193976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.153654 restraints weight = 34048.533| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.01 r_work: 0.3611 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11097 Z= 0.114 Angle : 0.467 4.850 15078 Z= 0.246 Chirality : 0.036 0.144 1698 Planarity : 0.004 0.047 1844 Dihedral : 7.954 81.690 1544 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.32 % Allowed : 6.60 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.91 (0.23), residues: 1348 helix: 1.59 (0.18), residues: 842 sheet: -2.03 (1.01), residues: 30 loop : -0.99 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 403 HIS 0.003 0.001 HIS B 787 PHE 0.010 0.001 PHE B 377 TYR 0.018 0.001 TYR B 211 ARG 0.004 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 645) hydrogen bonds : angle 4.71213 ( 1908) SS BOND : bond 0.00140 ( 6) SS BOND : angle 0.28453 ( 12) covalent geometry : bond 0.00253 (11090) covalent geometry : angle 0.46737 (15066) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 MET cc_start: 0.7775 (ptt) cc_final: 0.7550 (ptt) REVERT: B 757 MET cc_start: 0.7060 (mmm) cc_final: 0.6858 (mmt) outliers start: 15 outliers final: 12 residues processed: 144 average time/residue: 0.5163 time to fit residues: 108.9772 Evaluate side-chains 138 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 774 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.194396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.151058 restraints weight = 34472.377| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.25 r_work: 0.3514 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11097 Z= 0.158 Angle : 0.486 4.779 15078 Z= 0.255 Chirality : 0.037 0.143 1698 Planarity : 0.004 0.049 1844 Dihedral : 7.766 83.341 1544 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.50 % Allowed : 7.75 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.87 (0.23), residues: 1348 helix: 1.56 (0.18), residues: 842 sheet: -1.98 (1.00), residues: 30 loop : -1.03 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 403 HIS 0.004 0.001 HIS B 787 PHE 0.009 0.001 PHE B 251 TYR 0.017 0.001 TYR A 211 ARG 0.005 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 645) hydrogen bonds : angle 4.62301 ( 1908) SS BOND : bond 0.00195 ( 6) SS BOND : angle 0.36325 ( 12) covalent geometry : bond 0.00368 (11090) covalent geometry : angle 0.48560 (15066) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 TYR cc_start: 0.8333 (m-80) cc_final: 0.8077 (m-10) REVERT: A 683 MET cc_start: 0.7979 (ptt) cc_final: 0.7752 (ptt) REVERT: B 598 PHE cc_start: 0.6152 (t80) cc_final: 0.5928 (t80) outliers start: 17 outliers final: 15 residues processed: 138 average time/residue: 0.5083 time to fit residues: 101.6654 Evaluate side-chains 141 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 774 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.192632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.152000 restraints weight = 34331.511| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.06 r_work: 0.3556 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11097 Z= 0.159 Angle : 0.486 4.897 15078 Z= 0.255 Chirality : 0.037 0.145 1698 Planarity : 0.004 0.049 1844 Dihedral : 7.550 84.855 1544 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.32 % Allowed : 9.15 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.82 (0.23), residues: 1348 helix: 1.52 (0.18), residues: 842 sheet: -1.93 (1.01), residues: 30 loop : -1.04 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 403 HIS 0.004 0.001 HIS B 787 PHE 0.009 0.001 PHE B 251 TYR 0.018 0.001 TYR A 211 ARG 0.005 0.000 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 645) hydrogen bonds : angle 4.56415 ( 1908) SS BOND : bond 0.00186 ( 6) SS BOND : angle 0.43566 ( 12) covalent geometry : bond 0.00366 (11090) covalent geometry : angle 0.48623 (15066) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 TYR cc_start: 0.8357 (m-80) cc_final: 0.8105 (m-10) REVERT: A 598 PHE cc_start: 0.6072 (t80) cc_final: 0.5856 (t80) REVERT: A 683 MET cc_start: 0.7936 (ptt) cc_final: 0.7717 (ptt) REVERT: B 598 PHE cc_start: 0.6126 (t80) cc_final: 0.5905 (t80) outliers start: 15 outliers final: 15 residues processed: 140 average time/residue: 0.5214 time to fit residues: 105.6505 Evaluate side-chains 145 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 774 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.192554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152733 restraints weight = 34089.040| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.97 r_work: 0.3571 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11097 Z= 0.153 Angle : 0.480 4.977 15078 Z= 0.252 Chirality : 0.037 0.146 1698 Planarity : 0.004 0.050 1844 Dihedral : 7.393 87.394 1544 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.50 % Allowed : 9.42 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.85 (0.23), residues: 1348 helix: 1.54 (0.18), residues: 842 sheet: -1.97 (1.02), residues: 30 loop : -1.04 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 403 HIS 0.004 0.001 HIS B 787 PHE 0.008 0.001 PHE B 377 TYR 0.018 0.001 TYR A 211 ARG 0.004 0.000 ARG A 752 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 645) hydrogen bonds : angle 4.51451 ( 1908) SS BOND : bond 0.00207 ( 6) SS BOND : angle 0.47684 ( 12) covalent geometry : bond 0.00352 (11090) covalent geometry : angle 0.48012 (15066) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 TYR cc_start: 0.8333 (m-80) cc_final: 0.8112 (m-10) REVERT: A 598 PHE cc_start: 0.6076 (t80) cc_final: 0.5858 (t80) REVERT: A 683 MET cc_start: 0.7951 (ptt) cc_final: 0.7710 (ptt) REVERT: B 447 TYR cc_start: 0.8442 (m-80) cc_final: 0.8223 (m-10) REVERT: B 598 PHE cc_start: 0.6093 (t80) cc_final: 0.5875 (t80) outliers start: 17 outliers final: 16 residues processed: 147 average time/residue: 0.5301 time to fit residues: 113.4778 Evaluate side-chains 149 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 774 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.187451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144053 restraints weight = 34272.475| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.91 r_work: 0.3433 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11097 Z= 0.212 Angle : 0.530 4.642 15078 Z= 0.281 Chirality : 0.039 0.154 1698 Planarity : 0.005 0.052 1844 Dihedral : 7.801 81.222 1544 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.85 % Allowed : 9.42 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.53 (0.23), residues: 1348 helix: 1.27 (0.18), residues: 842 sheet: -1.87 (1.03), residues: 30 loop : -1.12 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 403 HIS 0.004 0.001 HIS B 787 PHE 0.015 0.001 PHE A 251 TYR 0.025 0.002 TYR A 211 ARG 0.005 0.001 ARG B 752 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 645) hydrogen bonds : angle 4.64808 ( 1908) SS BOND : bond 0.00304 ( 6) SS BOND : angle 0.72659 ( 12) covalent geometry : bond 0.00496 (11090) covalent geometry : angle 0.52993 (15066) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 TYR cc_start: 0.8397 (m-80) cc_final: 0.8158 (m-10) REVERT: A 683 MET cc_start: 0.8007 (ptt) cc_final: 0.7763 (ptt) REVERT: B 447 TYR cc_start: 0.8524 (m-80) cc_final: 0.8281 (m-10) REVERT: B 782 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.6806 (pp30) outliers start: 21 outliers final: 20 residues processed: 145 average time/residue: 0.4912 time to fit residues: 102.6757 Evaluate side-chains 150 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 787 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 782 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 101 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.190319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.150449 restraints weight = 34177.319| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.99 r_work: 0.3577 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11097 Z= 0.126 Angle : 0.469 6.610 15078 Z= 0.246 Chirality : 0.036 0.144 1698 Planarity : 0.004 0.052 1844 Dihedral : 7.112 88.546 1544 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.50 % Allowed : 10.12 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.87 (0.24), residues: 1348 helix: 1.54 (0.18), residues: 842 sheet: -1.79 (1.05), residues: 30 loop : -1.00 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 403 HIS 0.005 0.001 HIS B 787 PHE 0.009 0.001 PHE A 706 TYR 0.017 0.001 TYR A 211 ARG 0.005 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 645) hydrogen bonds : angle 4.48506 ( 1908) SS BOND : bond 0.00177 ( 6) SS BOND : angle 0.48274 ( 12) covalent geometry : bond 0.00282 (11090) covalent geometry : angle 0.46944 (15066) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 TYR cc_start: 0.8285 (m-80) cc_final: 0.8081 (m-10) REVERT: A 598 PHE cc_start: 0.6038 (t80) cc_final: 0.5748 (t80) REVERT: A 683 MET cc_start: 0.8016 (ptt) cc_final: 0.7766 (ptt) REVERT: A 711 ASP cc_start: 0.6438 (m-30) cc_final: 0.6083 (m-30) REVERT: A 782 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.6440 (pp30) REVERT: B 598 PHE cc_start: 0.6075 (t80) cc_final: 0.5846 (t80) outliers start: 17 outliers final: 15 residues processed: 146 average time/residue: 0.6954 time to fit residues: 151.8362 Evaluate side-chains 147 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 774 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 23 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.196052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.156620 restraints weight = 33967.823| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.14 r_work: 0.3510 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11097 Z= 0.177 Angle : 0.500 4.750 15078 Z= 0.263 Chirality : 0.038 0.149 1698 Planarity : 0.004 0.052 1844 Dihedral : 7.202 85.867 1544 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.67 % Allowed : 10.04 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.73 (0.23), residues: 1348 helix: 1.44 (0.18), residues: 842 sheet: -1.85 (1.06), residues: 30 loop : -1.08 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 403 HIS 0.003 0.001 HIS B 787 PHE 0.010 0.001 PHE A 251 TYR 0.021 0.002 TYR A 211 ARG 0.005 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 645) hydrogen bonds : angle 4.53640 ( 1908) SS BOND : bond 0.00242 ( 6) SS BOND : angle 0.62229 ( 12) covalent geometry : bond 0.00411 (11090) covalent geometry : angle 0.50027 (15066) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 MET cc_start: 0.8010 (ptt) cc_final: 0.7781 (ptt) REVERT: A 782 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.6529 (pp30) REVERT: B 782 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.6693 (pp30) outliers start: 19 outliers final: 16 residues processed: 148 average time/residue: 0.5984 time to fit residues: 129.0473 Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 787 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 782 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.191470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151997 restraints weight = 34228.767| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.99 r_work: 0.3545 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11097 Z= 0.111 Angle : 0.457 4.915 15078 Z= 0.239 Chirality : 0.036 0.141 1698 Planarity : 0.004 0.051 1844 Dihedral : 6.588 86.837 1544 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.41 % Allowed : 10.30 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.06 (0.24), residues: 1348 helix: 1.70 (0.18), residues: 842 sheet: -1.80 (1.06), residues: 30 loop : -0.94 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 403 HIS 0.004 0.001 HIS B 787 PHE 0.008 0.001 PHE A 706 TYR 0.015 0.001 TYR A 211 ARG 0.006 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 645) hydrogen bonds : angle 4.40555 ( 1908) SS BOND : bond 0.00155 ( 6) SS BOND : angle 0.40917 ( 12) covalent geometry : bond 0.00245 (11090) covalent geometry : angle 0.45753 (15066) Misc. bond : bond 0.00017 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 PHE cc_start: 0.6099 (t80) cc_final: 0.5813 (t80) REVERT: A 683 MET cc_start: 0.8003 (ptt) cc_final: 0.7779 (ptt) REVERT: A 711 ASP cc_start: 0.6536 (m-30) cc_final: 0.6119 (m-30) REVERT: A 782 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.6425 (pp30) REVERT: B 598 PHE cc_start: 0.6116 (t80) cc_final: 0.5894 (t80) outliers start: 16 outliers final: 14 residues processed: 148 average time/residue: 0.5365 time to fit residues: 116.1960 Evaluate side-chains 147 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 774 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.189652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.149251 restraints weight = 34427.180| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.01 r_work: 0.3564 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11097 Z= 0.156 Angle : 0.484 4.616 15078 Z= 0.254 Chirality : 0.037 0.147 1698 Planarity : 0.004 0.051 1844 Dihedral : 6.770 89.545 1544 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.41 % Allowed : 10.48 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.94 (0.24), residues: 1348 helix: 1.62 (0.18), residues: 842 sheet: -1.83 (1.06), residues: 30 loop : -1.02 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 403 HIS 0.004 0.001 HIS B 787 PHE 0.008 0.001 PHE B 300 TYR 0.018 0.001 TYR A 211 ARG 0.006 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 645) hydrogen bonds : angle 4.44899 ( 1908) SS BOND : bond 0.00224 ( 6) SS BOND : angle 0.52431 ( 12) covalent geometry : bond 0.00360 (11090) covalent geometry : angle 0.48359 (15066) Misc. bond : bond 0.00022 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11382.04 seconds wall clock time: 198 minutes 36.48 seconds (11916.48 seconds total)