Starting phenix.real_space_refine on Wed May 21 14:57:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgj_36236/05_2025/8jgj_36236_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgj_36236/05_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_36236/05_2025/8jgj_36236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgj_36236/05_2025/8jgj_36236.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgj_36236/05_2025/8jgj_36236_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgj_36236/05_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-5687/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: 10.31, per 1000 atoms: 0.48 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: 5.86 Conformation dependent library (CDL) restraints added in 1.8 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: 1.61 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: 7.46 Time building geometry restraints manager: 7.04 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: 0.06 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: 0.730 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: 0.350 Extract box with map and model: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 45.710 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.260 ------------------------------------------------------------------------------- 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 : 1.522 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: 0.5396 time to fit residues: 117.8185 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 : 1.742 ------------------------------------------------------------------------------- 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 = 34294.816| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.05 r_work: 0.3577 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 1.629 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: 0.5175 time to fit residues: 109.6845 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 : 1.735 ------------------------------------------------------------------------------- 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: 0.4980 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.192118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.149557 restraints weight = 34190.418| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.24 r_work: 0.3513 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11097 Z= 0.149 Angle : 0.490 4.955 15078 Z= 0.258 Chirality : 0.037 0.145 1698 Planarity : 0.004 0.049 1844 Dihedral : 8.223 81.278 1544 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.58 % Allowed : 7.22 % Favored : 91.20 % 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: 0.72 (0.23), residues: 1348 helix: 1.43 (0.18), residues: 842 sheet: -2.00 (1.01), residues: 30 loop : -1.08 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 403 HIS 0.003 0.001 HIS B 787 PHE 0.009 0.001 PHE B 377 TYR 0.018 0.001 TYR B 211 ARG 0.003 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 645) hydrogen bonds : angle 4.78316 ( 1908) SS BOND : bond 0.00194 ( 6) SS BOND : angle 0.37376 ( 12) covalent geometry : bond 0.00340 (11090) covalent geometry : angle 0.48967 (15066) Misc. bond : bond 0.00028 ( 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 146 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.546 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: 0.7825 (ptt) cc_final: 0.7605 (ptt) REVERT: B 757 MET cc_start: 0.7104 (mmm) cc_final: 0.6890 (mmt) outliers start: 18 outliers final: 16 residues processed: 139 average time/residue: 0.4838 time to fit residues: 97.0995 Evaluate side-chains 142 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 116 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 50 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.201085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.161257 restraints weight = 33970.481| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.07 r_work: 0.3584 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1390 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= 0.116 Angle : 0.459 5.177 15078 Z= 0.240 Chirality : 0.036 0.140 1698 Planarity : 0.004 0.047 1844 Dihedral : 7.462 85.872 1544 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.41 % Allowed : 7.75 % Favored : 90.85 % 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: 1.02 (0.23), residues: 1348 helix: 1.67 (0.18), residues: 842 sheet: -1.90 (1.01), residues: 30 loop : -0.95 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 403 HIS 0.004 0.001 HIS B 787 PHE 0.010 0.001 PHE B 377 TYR 0.015 0.001 TYR A 211 ARG 0.005 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 645) hydrogen bonds : angle 4.53824 ( 1908) SS BOND : bond 0.00136 ( 6) SS BOND : angle 0.28328 ( 12) covalent geometry : bond 0.00261 (11090) covalent geometry : angle 0.45898 (15066) Misc. bond : bond 0.00022 ( 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 147 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 MET cc_start: 0.7894 (ptt) cc_final: 0.7681 (ptt) outliers start: 16 outliers final: 14 residues processed: 139 average time/residue: 0.5034 time to fit residues: 101.0604 Evaluate side-chains 138 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 611 MET 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 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: 0.9980 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.199994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.158848 restraints weight = 33820.673| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.22 r_work: 0.3525 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11097 Z= 0.148 Angle : 0.476 4.612 15078 Z= 0.249 Chirality : 0.037 0.145 1698 Planarity : 0.004 0.048 1844 Dihedral : 7.444 86.330 1544 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.32 % Allowed : 8.80 % Favored : 89.88 % 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: 1.00 (0.23), residues: 1348 helix: 1.67 (0.18), residues: 842 sheet: -1.92 (1.03), residues: 30 loop : -0.98 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 403 HIS 0.003 0.001 HIS B 787 PHE 0.009 0.001 PHE B 251 TYR 0.017 0.001 TYR A 211 ARG 0.004 0.000 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 645) hydrogen bonds : angle 4.52381 ( 1908) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.40633 ( 12) covalent geometry : bond 0.00341 (11090) covalent geometry : angle 0.47646 (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 148 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.625 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 598 PHE cc_start: 0.6088 (t80) cc_final: 0.5875 (t80) REVERT: A 683 MET cc_start: 0.7947 (ptt) cc_final: 0.7721 (ptt) REVERT: B 598 PHE cc_start: 0.6146 (t80) cc_final: 0.5928 (t80) outliers start: 15 outliers final: 15 residues processed: 141 average time/residue: 0.4882 time to fit residues: 99.0939 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 : 1.515 ------------------------------------------------------------------------------- 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: 0.6980 chunk 116 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.189581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.149353 restraints weight = 34165.304| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.96 r_work: 0.3561 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11097 Z= 0.177 Angle : 0.502 4.637 15078 Z= 0.265 Chirality : 0.038 0.149 1698 Planarity : 0.004 0.051 1844 Dihedral : 7.577 84.036 1544 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.58 % Allowed : 9.24 % Favored : 89.17 % 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: 0.74 (0.23), residues: 1348 helix: 1.45 (0.18), residues: 842 sheet: -2.00 (1.02), residues: 30 loop : -1.07 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 403 HIS 0.005 0.001 HIS B 787 PHE 0.013 0.001 PHE B 251 TYR 0.021 0.002 TYR A 211 ARG 0.005 0.001 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 645) hydrogen bonds : angle 4.59334 ( 1908) SS BOND : bond 0.00260 ( 6) SS BOND : angle 0.62678 ( 12) covalent geometry : bond 0.00413 (11090) covalent geometry : angle 0.50196 (15066) Misc. bond : bond 0.00020 ( 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 152 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.647 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: 0.6062 (t80) cc_final: 0.5833 (t80) REVERT: A 683 MET cc_start: 0.7971 (ptt) cc_final: 0.7729 (ptt) REVERT: B 598 PHE cc_start: 0.6092 (t80) cc_final: 0.5832 (t80) REVERT: B 675 MET cc_start: 0.3807 (ptp) cc_final: 0.3487 (ptp) outliers start: 18 outliers final: 17 residues processed: 144 average time/residue: 0.5122 time to fit residues: 105.3471 Evaluate side-chains 147 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 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 774 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.188789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.147251 restraints weight = 34256.276| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.10 r_work: 0.3523 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11097 Z= 0.195 Angle : 0.513 4.602 15078 Z= 0.271 Chirality : 0.038 0.152 1698 Planarity : 0.004 0.051 1844 Dihedral : 7.629 83.257 1544 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.94 % Allowed : 9.60 % Favored : 88.47 % 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: 0.61 (0.23), residues: 1348 helix: 1.34 (0.18), residues: 842 sheet: -1.87 (1.05), residues: 30 loop : -1.12 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 403 HIS 0.004 0.001 HIS B 787 PHE 0.011 0.001 PHE B 251 TYR 0.022 0.002 TYR A 211 ARG 0.005 0.000 ARG B 752 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 645) hydrogen bonds : angle 4.60620 ( 1908) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.64821 ( 12) covalent geometry : bond 0.00456 (11090) covalent geometry : angle 0.51330 (15066) Misc. bond : bond 0.00012 ( 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: 22 poor density : 133 time to evaluate : 1.751 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 683 MET cc_start: 0.8013 (ptt) cc_final: 0.7765 (ptt) REVERT: A 782 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.6443 (pp30) REVERT: B 782 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6806 (pp30) outliers start: 22 outliers final: 18 residues processed: 146 average time/residue: 0.5079 time to fit residues: 106.9723 Evaluate side-chains 149 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 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 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: 0.4980 chunk 101 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 81 optimal weight: 0.1980 chunk 125 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.197518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.157474 restraints weight = 33852.618| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.00 r_work: 0.3608 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11097 Z= 0.108 Angle : 0.454 5.208 15078 Z= 0.238 Chirality : 0.036 0.140 1698 Planarity : 0.004 0.050 1844 Dihedral : 6.836 88.280 1544 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.32 % Allowed : 10.56 % 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: 1.06 (0.24), residues: 1348 helix: 1.69 (0.18), residues: 842 sheet: -1.77 (1.07), residues: 30 loop : -0.93 (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 0.010 0.001 PHE B 300 TYR 0.015 0.001 TYR A 211 ARG 0.005 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 645) hydrogen bonds : angle 4.42381 ( 1908) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.41399 ( 12) covalent geometry : bond 0.00236 (11090) covalent geometry : angle 0.45433 (15066) Misc. bond : bond 0.00008 ( 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 157 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.629 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: symmetry clash revert: symmetry clash REVERT: A 598 PHE cc_start: 0.6008 (t80) cc_final: 0.5726 (t80) REVERT: A 683 MET cc_start: 0.8026 (ptt) cc_final: 0.7791 (ptt) REVERT: A 711 ASP cc_start: 0.6437 (m-30) cc_final: 0.6087 (m-30) REVERT: B 598 PHE cc_start: 0.6050 (t80) cc_final: 0.5834 (t80) REVERT: B 757 MET cc_start: 0.6988 (mmt) cc_final: 0.6780 (mmt) REVERT: B 782 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.6639 (pp30) outliers start: 15 outliers final: 12 residues processed: 150 average time/residue: 0.5212 time to fit residues: 113.1704 Evaluate side-chains 148 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 23 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.190099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.146606 restraints weight = 34335.549| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.23 r_work: 0.3567 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2091 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= 0.161 Angle : 0.485 5.182 15078 Z= 0.254 Chirality : 0.037 0.148 1698 Planarity : 0.004 0.051 1844 Dihedral : 6.978 88.203 1544 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.58 % Allowed : 10.04 % 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: 0.93 (0.24), residues: 1348 helix: 1.61 (0.18), residues: 842 sheet: -1.87 (1.07), residues: 30 loop : -1.02 (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 0.009 0.001 PHE A 251 TYR 0.019 0.001 TYR A 211 ARG 0.006 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 645) hydrogen bonds : angle 4.46405 ( 1908) SS BOND : bond 0.00225 ( 6) SS BOND : angle 0.52518 ( 12) covalent geometry : bond 0.00373 (11090) covalent geometry : angle 0.48477 (15066) Misc. bond : bond 0.00015 ( 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: 18 poor density : 136 time to evaluate : 1.634 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: 0.8377 (m-80) cc_final: 0.8085 (m-10) REVERT: A 598 PHE cc_start: 0.6151 (t80) cc_final: 0.5857 (t80) REVERT: A 683 MET cc_start: 0.8051 (ptt) cc_final: 0.7813 (ptt) REVERT: B 757 MET cc_start: 0.7049 (mmt) cc_final: 0.6848 (mmt) REVERT: B 782 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.6678 (pp30) outliers start: 18 outliers final: 15 residues processed: 147 average time/residue: 0.4860 time to fit residues: 103.4124 Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 86 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.198333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.159600 restraints weight = 34007.068| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.00 r_work: 0.3573 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11097 Z= 0.122 Angle : 0.460 4.488 15078 Z= 0.241 Chirality : 0.036 0.143 1698 Planarity : 0.004 0.050 1844 Dihedral : 6.613 87.610 1544 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.14 % Allowed : 10.83 % Favored : 88.03 % 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: 1.11 (0.24), residues: 1348 helix: 1.75 (0.18), residues: 842 sheet: -1.84 (1.07), residues: 30 loop : -0.95 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 403 HIS 0.004 0.001 HIS B 787 PHE 0.008 0.001 PHE A 706 TYR 0.016 0.001 TYR A 211 ARG 0.006 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 645) hydrogen bonds : angle 4.38534 ( 1908) SS BOND : bond 0.00169 ( 6) SS BOND : angle 0.43497 ( 12) covalent geometry : bond 0.00276 (11090) covalent geometry : angle 0.46026 (15066) Misc. bond : bond 0.00018 ( 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 148 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.636 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: 0.8350 (m-80) cc_final: 0.8083 (m-10) REVERT: A 502 GLN cc_start: 0.8562 (pt0) cc_final: 0.8176 (pt0) REVERT: A 598 PHE cc_start: 0.6108 (t80) cc_final: 0.5830 (t80) REVERT: A 683 MET cc_start: 0.8037 (ptt) cc_final: 0.7810 (ptt) REVERT: A 711 ASP cc_start: 0.6569 (m-30) cc_final: 0.6120 (m-30) REVERT: B 447 TYR cc_start: 0.8398 (m-80) cc_final: 0.8181 (m-10) REVERT: B 598 PHE cc_start: 0.6134 (t80) cc_final: 0.5859 (t80) REVERT: B 782 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.6587 (pp30) outliers start: 13 outliers final: 12 residues processed: 143 average time/residue: 0.5003 time to fit residues: 103.0921 Evaluate side-chains 147 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 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 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 114 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.189652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147948 restraints weight = 34645.633| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.11 r_work: 0.3442 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2228 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= 0.183 Angle : 0.505 4.662 15078 Z= 0.266 Chirality : 0.038 0.151 1698 Planarity : 0.004 0.051 1844 Dihedral : 6.965 87.004 1544 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.32 % Allowed : 10.56 % 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: 0.86 (0.23), residues: 1348 helix: 1.58 (0.18), residues: 832 sheet: -1.89 (1.06), residues: 30 loop : -1.04 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 403 HIS 0.003 0.001 HIS B 787 PHE 0.012 0.001 PHE A 393 TYR 0.021 0.002 TYR A 211 ARG 0.006 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 645) hydrogen bonds : angle 4.49480 ( 1908) SS BOND : bond 0.00254 ( 6) SS BOND : angle 0.58871 ( 12) covalent geometry : bond 0.00427 (11090) covalent geometry : angle 0.50531 (15066) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10646.35 seconds wall clock time: 183 minutes 0.74 seconds (10980.74 seconds total)