Starting phenix.real_space_refine on Thu Jul 2 18:12:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wsu_32767/07_2026/7wsu_32767.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsu_32767/07_2026/7wsu_32767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsu_32767/07_2026/7wsu_32767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsu_32767/07_2026/7wsu_32767.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsu_32767/07_2026/7wsu_32767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsu_32767/07_2026/7wsu_32767.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wsu_32767/07_2026/7wsu_32767.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wsu_32767/07_2026/7wsu_32767.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.077 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: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 74 5.16 5 C 6316 2.51 5 N 1454 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9440 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4627 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 29, 'TRANS': 571} Chain breaks: 1 Chain: "B" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4627 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 29, 'TRANS': 571} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {' FE': 1, '5ZS': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {' FE': 1, '5ZS': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.43, per 1000 atoms: 0.26 Number of scatterers: 9440 At special positions: 0 Unit cell: (88.6495, 125.103, 82.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 74 16.00 O 1594 8.00 N 1454 7.00 C 6316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 250 " - pdb=" SG CYS B 671 " 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=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 343.9 milliseconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 1 sheets defined 78.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 50 through 73 Processing helix chain 'A' and resid 81 through 103 Processing helix chain 'A' and resid 111 through 132 removed outlier: 3.999A pdb=" N ILE A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.605A pdb=" N GLY A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 192 removed outlier: 3.585A pdb=" N CYS A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLY A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 179 " --> pdb=" O CYS A 175 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.877A pdb=" N GLN A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 Processing helix chain 'A' and resid 219 through 243 removed outlier: 4.276A pdb=" N PHE A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 265 removed outlier: 3.538A pdb=" N GLN A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 282 removed outlier: 3.799A pdb=" N ILE A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 300 through 307 Processing helix chain 'A' and resid 325 through 359 removed outlier: 3.619A pdb=" N LYS A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.892A pdb=" N TYR A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 420 through 446 removed outlier: 3.780A pdb=" N VAL A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Proline residue: A 432 - end of helix removed outlier: 3.560A pdb=" N ALA A 437 " --> pdb=" O MET A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 470 through 501 removed outlier: 3.611A pdb=" N SER A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 534 Proline residue: A 524 - end of helix Processing helix chain 'A' and resid 545 through 559 removed outlier: 3.965A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 removed outlier: 3.531A pdb=" N VAL A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 590 removed outlier: 3.543A pdb=" N MET A 590 " --> pdb=" O THR A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 removed outlier: 3.553A pdb=" N LYS A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 612 through 632 Processing helix chain 'A' and resid 632 through 664 removed outlier: 4.122A pdb=" N PHE A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Proline residue: A 641 - end of helix removed outlier: 4.211A pdb=" N PHE A 656 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Proline residue: A 657 - end of helix Processing helix chain 'B' and resid 50 through 73 Processing helix chain 'B' and resid 81 through 103 Processing helix chain 'B' and resid 111 through 132 removed outlier: 3.999A pdb=" N ILE B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA B 129 " --> pdb=" O CYS B 125 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE B 130 " --> pdb=" O TYR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.605A pdb=" N GLY B 150 " --> pdb=" O TYR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 192 removed outlier: 3.585A pdb=" N CYS B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY B 179 " --> pdb=" O CYS B 175 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 3.878A pdb=" N GLN B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 Processing helix chain 'B' and resid 219 through 243 removed outlier: 4.276A pdb=" N PHE B 243 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 265 removed outlier: 3.537A pdb=" N GLN B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 282 removed outlier: 3.799A pdb=" N ILE B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 299 Processing helix chain 'B' and resid 300 through 307 Processing helix chain 'B' and resid 325 through 359 removed outlier: 3.619A pdb=" N LYS B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 410 removed outlier: 3.892A pdb=" N TYR B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 420 through 446 removed outlier: 3.780A pdb=" N VAL B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.559A pdb=" N ALA B 437 " --> pdb=" O MET B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 464 Processing helix chain 'B' and resid 470 through 501 removed outlier: 3.611A pdb=" N SER B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP B 494 " --> pdb=" O ASP B 490 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 534 Proline residue: B 524 - end of helix Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.962A pdb=" N LEU B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 565 removed outlier: 3.533A pdb=" N VAL B 564 " --> pdb=" O GLY B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 590 removed outlier: 3.543A pdb=" N MET B 590 " --> pdb=" O THR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 596 removed outlier: 3.553A pdb=" N LYS B 596 " --> pdb=" O HIS B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 606 through 609 Processing helix chain 'B' and resid 612 through 632 Processing helix chain 'B' and resid 632 through 664 removed outlier: 4.121A pdb=" N PHE B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Proline residue: B 641 - end of helix removed outlier: 4.213A pdb=" N PHE B 656 " --> pdb=" O GLY B 652 " (cutoff:3.500A) Proline residue: B 657 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 671 through 675 640 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2734 1.34 - 1.46: 1946 1.46 - 1.57: 4906 1.57 - 1.69: 6 1.69 - 1.81: 126 Bond restraints: 9718 Sorted by residual: bond pdb=" C3 5ZS A 803 " pdb=" C4 5ZS A 803 " ideal model delta sigma weight residual 1.538 1.309 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C3 5ZS B 704 " pdb=" C4 5ZS B 704 " ideal model delta sigma weight residual 1.538 1.310 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C2 5ZS A 803 " pdb=" C3 5ZS A 803 " ideal model delta sigma weight residual 1.536 1.675 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C2 5ZS B 704 " pdb=" C3 5ZS B 704 " ideal model delta sigma weight residual 1.536 1.675 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C5 5ZS A 803 " pdb=" N1 5ZS A 803 " ideal model delta sigma weight residual 1.451 1.579 -0.128 2.00e-02 2.50e+03 4.11e+01 ... (remaining 9713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 13021 2.39 - 4.78: 153 4.78 - 7.17: 34 7.17 - 9.56: 6 9.56 - 11.95: 12 Bond angle restraints: 13226 Sorted by residual: angle pdb=" OAG Y01 B 701 " pdb=" CAY Y01 B 701 " pdb=" OAW Y01 B 701 " ideal model delta sigma weight residual 123.38 111.43 11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" OAG Y01 A 804 " pdb=" CAY Y01 A 804 " pdb=" OAW Y01 A 804 " ideal model delta sigma weight residual 123.38 111.43 11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" OAG Y01 A 801 " pdb=" CAY Y01 A 801 " pdb=" OAW Y01 A 801 " ideal model delta sigma weight residual 123.38 111.44 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" OAG Y01 B 702 " pdb=" CAY Y01 B 702 " pdb=" OAW Y01 B 702 " ideal model delta sigma weight residual 123.38 111.47 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CAM Y01 A 804 " pdb=" CAY Y01 A 804 " pdb=" OAW Y01 A 804 " ideal model delta sigma weight residual 111.19 122.92 -11.73 3.00e+00 1.11e-01 1.53e+01 ... (remaining 13221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 5047 15.77 - 31.54: 399 31.54 - 47.31: 102 47.31 - 63.08: 14 63.08 - 78.85: 12 Dihedral angle restraints: 5574 sinusoidal: 2162 harmonic: 3412 Sorted by residual: dihedral pdb=" CB CYS B 250 " pdb=" SG CYS B 250 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -148.88 62.88 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CB CYS A 250 " pdb=" SG CYS A 250 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -148.85 62.85 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CA LYS A 593 " pdb=" C LYS A 593 " pdb=" N TYR A 594 " pdb=" CA TYR A 594 " ideal model delta harmonic sigma weight residual 180.00 157.83 22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1179 0.049 - 0.098: 261 0.098 - 0.147: 44 0.147 - 0.197: 6 0.197 - 0.246: 4 Chirality restraints: 1494 Sorted by residual: chirality pdb=" C8 5ZS B 704 " pdb=" C7 5ZS B 704 " pdb=" C9 5ZS B 704 " pdb=" N2 5ZS B 704 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C8 5ZS A 803 " pdb=" C7 5ZS A 803 " pdb=" C9 5ZS A 803 " pdb=" N2 5ZS A 803 " both_signs ideal model delta sigma weight residual False -2.37 -2.61 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CBF Y01 B 702 " pdb=" CAS Y01 B 702 " pdb=" CBD Y01 B 702 " pdb=" CBH Y01 B 702 " both_signs ideal model delta sigma weight residual False -2.45 -2.67 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1491 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 523 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.06e+00 pdb=" N PRO A 524 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 524 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 524 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 523 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO B 524 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 606 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO A 607 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " -0.021 5.00e-02 4.00e+02 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 40 2.53 - 3.13: 7246 3.13 - 3.72: 14855 3.72 - 4.31: 21586 4.31 - 4.90: 35835 Nonbonded interactions: 79562 Sorted by model distance: nonbonded pdb="FE FE B 703 " pdb=" O1 5ZS B 704 " model vdw 1.943 2.260 nonbonded pdb="FE FE A 802 " pdb=" O1 5ZS A 803 " model vdw 1.944 2.260 nonbonded pdb="FE FE B 703 " pdb=" O5 5ZS B 704 " model vdw 1.971 2.260 nonbonded pdb="FE FE A 802 " pdb=" O5 5ZS A 803 " model vdw 1.971 2.260 nonbonded pdb="FE FE B 703 " pdb=" N2 5ZS B 704 " model vdw 2.032 2.340 ... (remaining 79557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 45 through 801) selection = (chain 'B' and resid 45 through 701) } 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: 5.230 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.970 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 : 0.006 0.229 9720 Z= 0.308 Angle : 0.736 11.947 13230 Z= 0.327 Chirality : 0.044 0.246 1494 Planarity : 0.005 0.075 1586 Dihedral : 12.638 78.854 3412 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.24), residues: 1194 helix: 0.97 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -1.17 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 221 TYR 0.012 0.001 TYR A 594 PHE 0.008 0.001 PHE A 130 TRP 0.009 0.001 TRP B 45 HIS 0.002 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.31 ( 9718) covalent geometry : angle 0.73630 / 0.33 (13226) SS BOND : bond 0.00057 / 0.03 ( 2) SS BOND : angle 0.99620 / 0.60 ( 4) hydrogen bonds : bond 0.24669 / 16.33 ( 640) hydrogen bonds : angle 7.23651 / 5.39 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.322 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.5525 time to fit residues: 94.7226 Evaluate side-chains 130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.0670 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 117 optimal weight: 0.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 512 GLN ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.154385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119442 restraints weight = 10453.851| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.88 r_work: 0.3150 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9720 Z= 0.141 Angle : 0.589 6.334 13230 Z= 0.301 Chirality : 0.042 0.146 1494 Planarity : 0.005 0.052 1586 Dihedral : 5.933 55.044 1398 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.87 % Allowed : 9.34 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.24), residues: 1194 helix: 1.75 (0.17), residues: 840 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 112 TYR 0.021 0.002 TYR B 343 PHE 0.011 0.001 PHE B 579 TRP 0.014 0.001 TRP B 654 HIS 0.002 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 9718) covalent geometry : angle 0.58837 / 0.30 (13226) SS BOND : bond 0.00127 / 0.06 ( 2) SS BOND : angle 1.07962 / 0.65 ( 4) hydrogen bonds : bond 0.05380 / 3.62 ( 640) hydrogen bonds : angle 4.58139 / 3.46 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.312 Fit side-chains REVERT: A 46 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.6036 (mp-120) REVERT: A 108 ARG cc_start: 0.6949 (tpp80) cc_final: 0.6716 (tpp80) REVERT: A 396 MET cc_start: 0.5796 (OUTLIER) cc_final: 0.5035 (tmm) REVERT: A 554 MET cc_start: 0.7878 (mtt) cc_final: 0.7637 (mtp) REVERT: B 46 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6029 (mp-120) REVERT: B 108 ARG cc_start: 0.6946 (tpp80) cc_final: 0.6711 (tpp80) REVERT: B 396 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5028 (tmm) REVERT: B 554 MET cc_start: 0.7895 (mtt) cc_final: 0.7653 (mtp) outliers start: 18 outliers final: 6 residues processed: 158 average time/residue: 0.4268 time to fit residues: 72.9364 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 586 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 14 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN B 452 ASN ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113863 restraints weight = 10037.459| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.92 r_work: 0.3096 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9720 Z= 0.145 Angle : 0.570 6.402 13230 Z= 0.283 Chirality : 0.041 0.136 1494 Planarity : 0.004 0.047 1586 Dihedral : 5.555 51.393 1398 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.90 % Allowed : 10.68 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.25), residues: 1194 helix: 1.91 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.75 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 112 TYR 0.018 0.002 TYR A 343 PHE 0.013 0.001 PHE A 331 TRP 0.015 0.001 TRP A 654 HIS 0.003 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 9718) covalent geometry : angle 0.56945 / 0.28 (13226) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 1.17426 / 0.70 ( 4) hydrogen bonds : bond 0.04889 / 3.32 ( 640) hydrogen bonds : angle 4.20422 / 3.18 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.211 Fit side-chains REVERT: A 108 ARG cc_start: 0.6876 (tpp80) cc_final: 0.6583 (tpp80) REVERT: A 396 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.5195 (tmt) REVERT: A 554 MET cc_start: 0.7976 (mtt) cc_final: 0.7763 (mtp) REVERT: B 108 ARG cc_start: 0.6888 (tpp80) cc_final: 0.6593 (tpp80) REVERT: B 396 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5205 (tmt) REVERT: B 554 MET cc_start: 0.8002 (mtt) cc_final: 0.7784 (mtp) outliers start: 28 outliers final: 10 residues processed: 142 average time/residue: 0.4595 time to fit residues: 70.3164 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 589 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 0.0670 chunk 97 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118401 restraints weight = 10310.005| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.92 r_work: 0.3064 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9720 Z= 0.140 Angle : 0.566 7.746 13230 Z= 0.282 Chirality : 0.042 0.197 1494 Planarity : 0.005 0.042 1586 Dihedral : 5.386 49.846 1398 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.07 % Allowed : 13.07 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.25), residues: 1194 helix: 1.95 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.68 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 98 TYR 0.016 0.001 TYR A 126 PHE 0.011 0.001 PHE A 614 TRP 0.015 0.001 TRP B 654 HIS 0.003 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9718) covalent geometry : angle 0.56530 / 0.28 (13226) SS BOND : bond 0.00096 / 0.05 ( 2) SS BOND : angle 1.18800 / 0.71 ( 4) hydrogen bonds : bond 0.04602 / 3.13 ( 640) hydrogen bonds : angle 4.11714 / 3.12 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.345 Fit side-chains REVERT: A 108 ARG cc_start: 0.6918 (tpp80) cc_final: 0.6638 (tpp80) REVERT: A 396 MET cc_start: 0.5861 (OUTLIER) cc_final: 0.5234 (tmt) REVERT: A 554 MET cc_start: 0.8065 (mtt) cc_final: 0.7835 (mtp) REVERT: A 663 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8104 (mp) REVERT: B 108 ARG cc_start: 0.6912 (tpp80) cc_final: 0.6622 (tpp80) REVERT: B 396 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5244 (tmt) REVERT: B 554 MET cc_start: 0.8065 (mtt) cc_final: 0.7832 (mtp) REVERT: B 663 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8093 (mp) outliers start: 20 outliers final: 8 residues processed: 135 average time/residue: 0.5511 time to fit residues: 79.8191 Evaluate side-chains 128 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.141326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.105264 restraints weight = 10585.371| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.74 r_work: 0.2969 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9720 Z= 0.196 Angle : 0.625 7.170 13230 Z= 0.312 Chirality : 0.044 0.145 1494 Planarity : 0.005 0.046 1586 Dihedral : 5.680 51.968 1398 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.11 % Allowed : 14.11 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.25), residues: 1194 helix: 1.78 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.85 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 98 TYR 0.017 0.002 TYR B 126 PHE 0.013 0.002 PHE A 331 TRP 0.013 0.001 TRP B 167 HIS 0.005 0.002 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 ( 9718) covalent geometry : angle 0.62448 / 0.31 (13226) SS BOND : bond 0.00035 / 0.02 ( 2) SS BOND : angle 1.39154 / 0.80 ( 4) hydrogen bonds : bond 0.05295 / 3.63 ( 640) hydrogen bonds : angle 4.22118 / 3.20 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.265 Fit side-chains REVERT: A 88 LEU cc_start: 0.8387 (mp) cc_final: 0.7998 (tt) REVERT: A 108 ARG cc_start: 0.6960 (tpp80) cc_final: 0.6605 (tpp80) REVERT: A 182 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8079 (p) REVERT: A 356 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6893 (pp-130) REVERT: A 396 MET cc_start: 0.5941 (OUTLIER) cc_final: 0.5323 (tmt) REVERT: A 538 ASN cc_start: 0.7990 (t0) cc_final: 0.7722 (m-40) REVERT: A 663 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8218 (mp) REVERT: B 88 LEU cc_start: 0.8395 (mp) cc_final: 0.8007 (tt) REVERT: B 108 ARG cc_start: 0.6952 (tpp80) cc_final: 0.6598 (tpp80) REVERT: B 356 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6894 (pp-130) REVERT: B 396 MET cc_start: 0.5923 (OUTLIER) cc_final: 0.5306 (tmt) REVERT: B 538 ASN cc_start: 0.7977 (t0) cc_final: 0.7714 (m-40) REVERT: B 663 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8221 (mp) outliers start: 30 outliers final: 11 residues processed: 148 average time/residue: 0.4734 time to fit residues: 75.2461 Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 85 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 0.0470 chunk 113 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN B 115 ASN ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.144355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108746 restraints weight = 10541.576| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.74 r_work: 0.3017 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9720 Z= 0.131 Angle : 0.557 7.958 13230 Z= 0.276 Chirality : 0.041 0.129 1494 Planarity : 0.005 0.043 1586 Dihedral : 5.248 48.416 1398 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.07 % Allowed : 17.43 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.25), residues: 1194 helix: 2.00 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.73 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 98 TYR 0.014 0.001 TYR B 126 PHE 0.013 0.001 PHE A 614 TRP 0.017 0.001 TRP A 654 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9718) covalent geometry : angle 0.55670 / 0.28 (13226) SS BOND : bond 0.00106 / 0.05 ( 2) SS BOND : angle 1.26183 / 0.77 ( 4) hydrogen bonds : bond 0.04418 / 3.01 ( 640) hydrogen bonds : angle 4.07001 / 3.10 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.360 Fit side-chains REVERT: A 88 LEU cc_start: 0.8371 (mp) cc_final: 0.7988 (tt) REVERT: A 108 ARG cc_start: 0.6966 (tpp80) cc_final: 0.6717 (tpp80) REVERT: A 396 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.5292 (tmt) REVERT: A 538 ASN cc_start: 0.7927 (t0) cc_final: 0.7576 (m-40) REVERT: A 663 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 88 LEU cc_start: 0.8374 (mp) cc_final: 0.7992 (tt) REVERT: B 108 ARG cc_start: 0.6962 (tpp80) cc_final: 0.6712 (tpp80) REVERT: B 396 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.5280 (tmt) REVERT: B 538 ASN cc_start: 0.7938 (t0) cc_final: 0.7583 (m-40) REVERT: B 663 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8156 (mp) outliers start: 20 outliers final: 8 residues processed: 143 average time/residue: 0.5323 time to fit residues: 81.8658 Evaluate side-chains 130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 94 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 11 optimal weight: 0.0070 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.145594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.110164 restraints weight = 10577.455| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.72 r_work: 0.3041 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9720 Z= 0.122 Angle : 0.563 8.610 13230 Z= 0.277 Chirality : 0.040 0.126 1494 Planarity : 0.005 0.041 1586 Dihedral : 5.049 44.787 1398 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.70 % Allowed : 17.43 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.25), residues: 1194 helix: 2.12 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.63 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 98 TYR 0.014 0.002 TYR A 453 PHE 0.012 0.001 PHE A 614 TRP 0.018 0.001 TRP B 654 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9718) covalent geometry : angle 0.56301 / 0.28 (13226) SS BOND : bond 0.00088 / 0.04 ( 2) SS BOND : angle 1.22439 / 0.74 ( 4) hydrogen bonds : bond 0.04197 / 2.86 ( 640) hydrogen bonds : angle 4.00367 / 3.04 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.345 Fit side-chains REVERT: A 88 LEU cc_start: 0.8376 (mp) cc_final: 0.7977 (tt) REVERT: A 108 ARG cc_start: 0.7008 (tpp80) cc_final: 0.6745 (tpp80) REVERT: A 396 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5366 (tmt) REVERT: A 538 ASN cc_start: 0.7890 (t0) cc_final: 0.7556 (m-40) REVERT: A 663 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8104 (mp) REVERT: B 88 LEU cc_start: 0.8373 (mp) cc_final: 0.7978 (tt) REVERT: B 108 ARG cc_start: 0.7006 (tpp80) cc_final: 0.6746 (tpp80) REVERT: B 396 MET cc_start: 0.5976 (OUTLIER) cc_final: 0.5355 (tmt) REVERT: B 538 ASN cc_start: 0.7896 (t0) cc_final: 0.7573 (m-40) REVERT: B 663 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8111 (mp) outliers start: 26 outliers final: 10 residues processed: 142 average time/residue: 0.5153 time to fit residues: 78.6318 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.157215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124651 restraints weight = 10178.272| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.64 r_work: 0.3272 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9720 Z= 0.162 Angle : 0.604 8.898 13230 Z= 0.299 Chirality : 0.042 0.133 1494 Planarity : 0.005 0.044 1586 Dihedral : 5.243 45.811 1398 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.87 % Allowed : 18.57 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.25), residues: 1194 helix: 2.00 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.75 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 98 TYR 0.016 0.002 TYR B 126 PHE 0.011 0.001 PHE A 331 TRP 0.014 0.001 TRP B 654 HIS 0.003 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 9718) covalent geometry : angle 0.60377 / 0.30 (13226) SS BOND : bond 0.00036 / 0.02 ( 2) SS BOND : angle 1.33578 / 0.78 ( 4) hydrogen bonds : bond 0.04744 / 3.26 ( 640) hydrogen bonds : angle 4.08262 / 3.10 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.298 Fit side-chains REVERT: A 88 LEU cc_start: 0.8533 (mp) cc_final: 0.8174 (tt) REVERT: A 108 ARG cc_start: 0.7081 (tpp80) cc_final: 0.6838 (tpp80) REVERT: A 193 ASP cc_start: 0.8781 (t0) cc_final: 0.8521 (m-30) REVERT: A 396 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5403 (tmt) REVERT: A 538 ASN cc_start: 0.8013 (t0) cc_final: 0.7678 (m-40) REVERT: A 663 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8363 (mp) REVERT: B 88 LEU cc_start: 0.8532 (mp) cc_final: 0.8174 (tt) REVERT: B 108 ARG cc_start: 0.7069 (tpp80) cc_final: 0.6823 (tpp80) REVERT: B 193 ASP cc_start: 0.8784 (t0) cc_final: 0.8526 (m-30) REVERT: B 396 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5396 (tmt) REVERT: B 538 ASN cc_start: 0.8006 (t0) cc_final: 0.7678 (m-40) REVERT: B 663 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8374 (mp) outliers start: 18 outliers final: 8 residues processed: 140 average time/residue: 0.4954 time to fit residues: 74.7345 Evaluate side-chains 138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 85 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.0030 chunk 55 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126386 restraints weight = 10230.156| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.65 r_work: 0.3300 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9720 Z= 0.134 Angle : 0.583 8.472 13230 Z= 0.287 Chirality : 0.040 0.128 1494 Planarity : 0.005 0.042 1586 Dihedral : 5.027 43.114 1398 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.45 % Allowed : 19.19 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.25), residues: 1194 helix: 2.12 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.66 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 98 TYR 0.014 0.002 TYR A 126 PHE 0.011 0.001 PHE A 614 TRP 0.016 0.001 TRP A 654 HIS 0.002 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9718) covalent geometry : angle 0.58260 / 0.29 (13226) SS BOND : bond 0.00082 / 0.04 ( 2) SS BOND : angle 1.24166 / 0.75 ( 4) hydrogen bonds : bond 0.04321 / 2.95 ( 640) hydrogen bonds : angle 4.02019 / 3.05 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.344 Fit side-chains REVERT: A 88 LEU cc_start: 0.8537 (mp) cc_final: 0.8184 (tt) REVERT: A 108 ARG cc_start: 0.7084 (tpp80) cc_final: 0.6844 (tpp80) REVERT: A 193 ASP cc_start: 0.8782 (t0) cc_final: 0.8514 (m-30) REVERT: A 396 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5423 (tmt) REVERT: A 538 ASN cc_start: 0.7966 (t0) cc_final: 0.7677 (m110) REVERT: A 663 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8312 (mp) REVERT: B 88 LEU cc_start: 0.8539 (mp) cc_final: 0.8186 (tt) REVERT: B 108 ARG cc_start: 0.7072 (tpp80) cc_final: 0.6830 (tpp80) REVERT: B 193 ASP cc_start: 0.8801 (t0) cc_final: 0.8524 (m-30) REVERT: B 396 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.5420 (tmt) REVERT: B 538 ASN cc_start: 0.7958 (t0) cc_final: 0.7674 (m110) REVERT: B 663 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8324 (mp) outliers start: 14 outliers final: 8 residues processed: 136 average time/residue: 0.4783 time to fit residues: 69.9810 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.0060 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126962 restraints weight = 10227.581| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.64 r_work: 0.3308 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9720 Z= 0.130 Angle : 0.574 8.193 13230 Z= 0.283 Chirality : 0.040 0.128 1494 Planarity : 0.005 0.042 1586 Dihedral : 4.934 40.269 1398 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.45 % Allowed : 18.98 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.25), residues: 1194 helix: 2.15 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.61 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 98 TYR 0.014 0.001 TYR A 126 PHE 0.011 0.001 PHE A 614 TRP 0.016 0.001 TRP B 654 HIS 0.002 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9718) covalent geometry : angle 0.57373 / 0.28 (13226) SS BOND : bond 0.00068 / 0.03 ( 2) SS BOND : angle 1.23266 / 0.74 ( 4) hydrogen bonds : bond 0.04255 / 2.91 ( 640) hydrogen bonds : angle 3.99279 / 3.03 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.285 Fit side-chains REVERT: A 88 LEU cc_start: 0.8544 (mp) cc_final: 0.8186 (tt) REVERT: A 108 ARG cc_start: 0.7074 (tpp80) cc_final: 0.6838 (tpp80) REVERT: A 356 MET cc_start: 0.7296 (ppp) cc_final: 0.7036 (pp-130) REVERT: A 396 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.5455 (tmt) REVERT: A 506 LYS cc_start: 0.8180 (mttt) cc_final: 0.7856 (mtmt) REVERT: A 538 ASN cc_start: 0.7955 (t0) cc_final: 0.7691 (m110) REVERT: A 663 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8337 (mp) REVERT: B 88 LEU cc_start: 0.8556 (mp) cc_final: 0.8200 (tt) REVERT: B 108 ARG cc_start: 0.7070 (tpp80) cc_final: 0.6830 (tpp80) REVERT: B 356 MET cc_start: 0.7326 (ppp) cc_final: 0.7057 (pp-130) REVERT: B 396 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5449 (tmt) REVERT: B 506 LYS cc_start: 0.8163 (mttt) cc_final: 0.7845 (mtmt) REVERT: B 538 ASN cc_start: 0.7949 (t0) cc_final: 0.7682 (m110) REVERT: B 663 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8348 (mp) outliers start: 14 outliers final: 10 residues processed: 140 average time/residue: 0.4525 time to fit residues: 68.3479 Evaluate side-chains 138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120954 restraints weight = 10279.346| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.69 r_work: 0.3273 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9720 Z= 0.162 Angle : 0.606 9.292 13230 Z= 0.299 Chirality : 0.042 0.132 1494 Planarity : 0.005 0.044 1586 Dihedral : 5.158 41.925 1398 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.76 % Allowed : 18.88 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.25), residues: 1194 helix: 2.04 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.71 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 98 TYR 0.016 0.002 TYR A 126 PHE 0.011 0.001 PHE A 331 TRP 0.014 0.001 TRP B 654 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 9718) covalent geometry : angle 0.60550 / 0.30 (13226) SS BOND : bond 0.00029 / 0.01 ( 2) SS BOND : angle 1.28961 / 0.75 ( 4) hydrogen bonds : bond 0.04733 / 3.25 ( 640) hydrogen bonds : angle 4.08868 / 3.10 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3045.73 seconds wall clock time: 52 minutes 44.66 seconds (3164.66 seconds total)