Starting phenix.real_space_refine on Tue Nov 18 00:46:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsu_32767/11_2025/7wsu_32767.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsu_32767/11_2025/7wsu_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wsu_32767/11_2025/7wsu_32767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsu_32767/11_2025/7wsu_32767.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wsu_32767/11_2025/7wsu_32767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsu_32767/11_2025/7wsu_32767.map" } 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-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9440 Number of models: 1 Model: "" Number of chains: 3 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: "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} Restraints were copied for chains: B Time building chain proxies: 3.91, per 1000 atoms: 0.41 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: 0.83 Conformation dependent library (CDL) restraints added in 358.8 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: 0.29 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: 1.59 Time building geometry restraints manager: 1.11 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: 5241 15.77 - 31.54: 421 31.54 - 47.31: 114 47.31 - 63.08: 18 63.08 - 78.85: 12 Dihedral angle restraints: 5806 sinusoidal: 2394 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 5803 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: 0.01 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: 5.180 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.640 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 12.785 78.854 3644 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 covalent geometry : bond 0.00625 ( 9718) covalent geometry : angle 0.73630 (13226) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.99620 ( 4) hydrogen bonds : bond 0.24669 ( 640) hydrogen bonds : angle 7.23651 ( 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 : 0.381 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.5959 time to fit residues: 101.8607 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 : 0.345 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3770 r_free = 0.3770 target = 0.155901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120337 restraints weight = 10413.669| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.92 r_work: 0.3125 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9720 Z= 0.142 Angle : 0.586 6.087 13230 Z= 0.299 Chirality : 0.042 0.141 1494 Planarity : 0.005 0.052 1586 Dihedral : 7.827 58.381 1630 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.66 % Allowed : 9.54 % 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: 1.58 (0.24), residues: 1194 helix: 1.77 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.68 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 112 TYR 0.020 0.002 TYR B 343 PHE 0.012 0.001 PHE B 579 TRP 0.013 0.001 TRP B 654 HIS 0.002 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9718) covalent geometry : angle 0.58540 (13226) SS BOND : bond 0.00108 ( 2) SS BOND : angle 1.09985 ( 4) hydrogen bonds : bond 0.05575 ( 640) hydrogen bonds : angle 4.59749 ( 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 164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.363 Fit side-chains REVERT: A 46 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.6029 (mp-120) REVERT: A 108 ARG cc_start: 0.6944 (tpp80) cc_final: 0.6740 (tpp80) REVERT: A 396 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.5030 (tmm) REVERT: A 554 MET cc_start: 0.7881 (mtt) cc_final: 0.7589 (mtp) REVERT: B 46 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6021 (mp-120) REVERT: B 108 ARG cc_start: 0.6962 (tpp80) cc_final: 0.6756 (tpp80) REVERT: B 396 MET cc_start: 0.5787 (OUTLIER) cc_final: 0.5022 (tmm) REVERT: B 554 MET cc_start: 0.7895 (mtt) cc_final: 0.7601 (mtp) outliers start: 16 outliers final: 6 residues processed: 156 average time/residue: 0.5160 time to fit residues: 86.9718 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 : 0.362 ------------------------------------------------------------------------------- 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: 4.9990 chunk 52 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 26 optimal weight: 0.3980 chunk 14 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3740 r_free = 0.3740 target = 0.153291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117382 restraints weight = 10072.957| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.87 r_work: 0.3137 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9720 Z= 0.127 Angle : 0.547 6.534 13230 Z= 0.273 Chirality : 0.040 0.131 1494 Planarity : 0.004 0.045 1586 Dihedral : 7.448 57.286 1630 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.49 % Allowed : 11.10 % 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: 1.80 (0.25), residues: 1194 helix: 1.96 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.017 0.002 TYR A 343 PHE 0.011 0.001 PHE A 331 TRP 0.016 0.001 TRP B 654 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9718) covalent geometry : angle 0.54633 (13226) SS BOND : bond 0.00163 ( 2) SS BOND : angle 1.11734 ( 4) hydrogen bonds : bond 0.04705 ( 640) hydrogen bonds : angle 4.21516 ( 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: 24 poor density : 134 time to evaluate : 0.349 Fit side-chains REVERT: A 46 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6551 (mp10) REVERT: A 108 ARG cc_start: 0.6941 (tpp80) cc_final: 0.6653 (tpp80) REVERT: A 396 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5181 (tmt) REVERT: A 554 MET cc_start: 0.7938 (mtt) cc_final: 0.7717 (mtp) REVERT: B 46 GLN cc_start: 0.6785 (OUTLIER) cc_final: 0.6576 (mp10) REVERT: B 108 ARG cc_start: 0.6943 (tpp80) cc_final: 0.6652 (tpp80) REVERT: B 396 MET cc_start: 0.5842 (OUTLIER) cc_final: 0.5185 (tmt) REVERT: B 554 MET cc_start: 0.7966 (mtt) cc_final: 0.7740 (mtp) outliers start: 24 outliers final: 8 residues processed: 144 average time/residue: 0.5718 time to fit residues: 88.4569 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 : 0.360 ------------------------------------------------------------------------------- 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 197 VAL 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 46 GLN 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 589 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 0.0970 chunk 109 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 112 optimal weight: 0.0010 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.154860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119195 restraints weight = 10356.683| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.88 r_work: 0.3162 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2050 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= 0.129 Angle : 0.557 7.205 13230 Z= 0.278 Chirality : 0.041 0.185 1494 Planarity : 0.004 0.042 1586 Dihedral : 7.225 56.692 1630 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.39 % Allowed : 12.66 % Favored : 84.96 % 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: 1.92 (0.25), residues: 1194 helix: 2.05 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 98 TYR 0.016 0.001 TYR A 126 PHE 0.010 0.001 PHE A 614 TRP 0.015 0.001 TRP B 654 HIS 0.002 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9718) covalent geometry : angle 0.55647 (13226) SS BOND : bond 0.00124 ( 2) SS BOND : angle 1.14058 ( 4) hydrogen bonds : bond 0.04427 ( 640) hydrogen bonds : angle 4.07551 ( 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 148 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.351 Fit side-chains REVERT: A 108 ARG cc_start: 0.6918 (tpp80) cc_final: 0.6648 (tpp80) REVERT: A 396 MET cc_start: 0.5891 (OUTLIER) cc_final: 0.5274 (tmt) REVERT: A 554 MET cc_start: 0.7956 (mtt) cc_final: 0.7726 (mtp) REVERT: B 108 ARG cc_start: 0.6908 (tpp80) cc_final: 0.6632 (tpp80) REVERT: B 396 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.5277 (tmt) REVERT: B 554 MET cc_start: 0.7953 (mtt) cc_final: 0.7724 (mtp) outliers start: 23 outliers final: 8 residues processed: 137 average time/residue: 0.5633 time to fit residues: 83.0243 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 596 LYS 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 Chi-restraints excluded: chain B residue 596 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 116 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.0020 chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 0.0020 chunk 100 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3770 r_free = 0.3770 target = 0.156384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120822 restraints weight = 10295.799| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.87 r_work: 0.3147 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2217 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= 0.115 Angle : 0.533 7.479 13230 Z= 0.264 Chirality : 0.040 0.156 1494 Planarity : 0.005 0.047 1586 Dihedral : 6.907 55.407 1630 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.49 % Allowed : 14.21 % Favored : 83.30 % 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: 2.08 (0.25), residues: 1194 helix: 2.19 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 98 TYR 0.015 0.001 TYR B 126 PHE 0.011 0.001 PHE A 614 TRP 0.017 0.001 TRP B 654 HIS 0.002 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9718) covalent geometry : angle 0.53267 (13226) SS BOND : bond 0.00106 ( 2) SS BOND : angle 1.08767 ( 4) hydrogen bonds : bond 0.04076 ( 640) hydrogen bonds : angle 3.96225 ( 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 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.356 Fit side-chains REVERT: A 70 LYS cc_start: 0.8400 (tttp) cc_final: 0.8196 (tmtt) REVERT: A 108 ARG cc_start: 0.6980 (tpp80) cc_final: 0.6658 (tpp80) REVERT: A 396 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5212 (tmt) REVERT: A 663 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8046 (mp) REVERT: B 70 LYS cc_start: 0.8395 (tttp) cc_final: 0.8190 (tmtt) REVERT: B 108 ARG cc_start: 0.6968 (tpp80) cc_final: 0.6646 (tpp80) REVERT: B 396 MET cc_start: 0.5850 (OUTLIER) cc_final: 0.5211 (tmt) REVERT: B 663 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8034 (mp) outliers start: 24 outliers final: 12 residues processed: 152 average time/residue: 0.5396 time to fit residues: 88.3646 Evaluate side-chains 141 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 325 LEU 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 182 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 311 ASP 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 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: 0.0670 chunk 63 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 113 optimal weight: 0.0970 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.155957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120371 restraints weight = 10294.236| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.86 r_work: 0.3143 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9720 Z= 0.135 Angle : 0.570 8.212 13230 Z= 0.280 Chirality : 0.041 0.149 1494 Planarity : 0.005 0.040 1586 Dihedral : 6.890 55.551 1630 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.07 % Allowed : 15.56 % Favored : 82.37 % 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: 2.17 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 98 TYR 0.016 0.001 TYR B 126 PHE 0.011 0.001 PHE A 331 TRP 0.015 0.001 TRP B 654 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9718) covalent geometry : angle 0.56981 (13226) SS BOND : bond 0.00096 ( 2) SS BOND : angle 1.14028 ( 4) hydrogen bonds : bond 0.04336 ( 640) hydrogen bonds : angle 3.97070 ( 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 154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.358 Fit side-chains REVERT: A 70 LYS cc_start: 0.8402 (tttp) cc_final: 0.8189 (tmtt) REVERT: A 108 ARG cc_start: 0.6986 (tpp80) cc_final: 0.6645 (tpp80) REVERT: A 193 ASP cc_start: 0.8667 (t0) cc_final: 0.8419 (m-30) REVERT: A 396 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5248 (tmt) REVERT: A 433 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8294 (ttm) REVERT: A 663 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8067 (mp) REVERT: B 70 LYS cc_start: 0.8392 (tttp) cc_final: 0.8179 (tmtt) REVERT: B 108 ARG cc_start: 0.6970 (tpp80) cc_final: 0.6625 (tpp80) REVERT: B 193 ASP cc_start: 0.8650 (t0) cc_final: 0.8402 (m-30) REVERT: B 396 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5246 (tmt) REVERT: B 433 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8293 (ttm) REVERT: B 663 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8052 (mp) outliers start: 20 outliers final: 10 residues processed: 144 average time/residue: 0.5848 time to fit residues: 90.3833 Evaluate side-chains 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU 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 433 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 148 LEU 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 433 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 94 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.151476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115964 restraints weight = 10263.543| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.84 r_work: 0.3082 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9720 Z= 0.164 Angle : 0.590 8.128 13230 Z= 0.294 Chirality : 0.042 0.137 1494 Planarity : 0.005 0.044 1586 Dihedral : 7.076 56.156 1630 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.70 % Allowed : 16.29 % Favored : 81.02 % 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: 2.07 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.80 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 98 TYR 0.017 0.002 TYR B 126 PHE 0.012 0.001 PHE A 331 TRP 0.013 0.001 TRP A 167 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9718) covalent geometry : angle 0.58984 (13226) SS BOND : bond 0.00055 ( 2) SS BOND : angle 1.20902 ( 4) hydrogen bonds : bond 0.04839 ( 640) hydrogen bonds : angle 4.07677 ( 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 160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.362 Fit side-chains REVERT: A 108 ARG cc_start: 0.7007 (tpp80) cc_final: 0.6636 (tpp80) REVERT: A 193 ASP cc_start: 0.8646 (t0) cc_final: 0.8396 (m-30) REVERT: A 396 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5353 (tmt) REVERT: A 538 ASN cc_start: 0.7962 (t0) cc_final: 0.7578 (m-40) REVERT: A 663 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8163 (mp) REVERT: B 108 ARG cc_start: 0.6996 (tpp80) cc_final: 0.6623 (tpp80) REVERT: B 193 ASP cc_start: 0.8650 (t0) cc_final: 0.8400 (m-30) REVERT: B 396 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.5360 (tmt) REVERT: B 538 ASN cc_start: 0.7969 (t0) cc_final: 0.7589 (m-40) REVERT: B 663 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8148 (mp) outliers start: 26 outliers final: 12 residues processed: 150 average time/residue: 0.5516 time to fit residues: 89.0399 Evaluate side-chains 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 192 VAL 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 596 LYS Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 VAL 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 596 LYS 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: 0.7980 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 0.0030 chunk 63 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.144651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109353 restraints weight = 10518.191| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.70 r_work: 0.3208 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9720 Z= 0.135 Angle : 0.586 9.120 13230 Z= 0.287 Chirality : 0.041 0.135 1494 Planarity : 0.005 0.046 1586 Dihedral : 6.852 53.763 1630 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.87 % Allowed : 17.01 % Favored : 81.12 % 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: 2.15 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 98 TYR 0.014 0.002 TYR A 126 PHE 0.012 0.001 PHE A 614 TRP 0.016 0.001 TRP B 654 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9718) covalent geometry : angle 0.58617 (13226) SS BOND : bond 0.00089 ( 2) SS BOND : angle 1.14587 ( 4) hydrogen bonds : bond 0.04382 ( 640) hydrogen bonds : angle 4.03132 ( 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 143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.331 Fit side-chains REVERT: A 88 LEU cc_start: 0.8444 (mp) cc_final: 0.8095 (tt) REVERT: A 108 ARG cc_start: 0.7055 (tpp80) cc_final: 0.6714 (tpp80) REVERT: A 193 ASP cc_start: 0.8719 (t0) cc_final: 0.8468 (m-30) REVERT: A 396 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5430 (tmt) REVERT: A 538 ASN cc_start: 0.7954 (t0) cc_final: 0.7651 (m-40) REVERT: A 663 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8172 (mp) REVERT: B 88 LEU cc_start: 0.8453 (mp) cc_final: 0.8105 (tt) REVERT: B 108 ARG cc_start: 0.7043 (tpp80) cc_final: 0.6703 (tpp80) REVERT: B 193 ASP cc_start: 0.8722 (t0) cc_final: 0.8463 (m-30) REVERT: B 396 MET cc_start: 0.6016 (OUTLIER) cc_final: 0.5423 (tmt) REVERT: B 538 ASN cc_start: 0.7967 (t0) cc_final: 0.7661 (m-40) REVERT: B 663 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8173 (mp) outliers start: 18 outliers final: 10 residues processed: 137 average time/residue: 0.5955 time to fit residues: 87.3229 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 192 VAL 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 192 VAL 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: 0.3980 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.144848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.108374 restraints weight = 10487.681| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.73 r_work: 0.3027 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2472 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= 0.137 Angle : 0.575 9.070 13230 Z= 0.283 Chirality : 0.041 0.131 1494 Planarity : 0.005 0.041 1586 Dihedral : 6.827 52.467 1630 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.28 % Allowed : 17.12 % Favored : 80.60 % 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: 2.05 (0.25), residues: 1194 helix: 2.16 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 98 TYR 0.015 0.002 TYR A 126 PHE 0.011 0.001 PHE A 614 TRP 0.015 0.001 TRP B 654 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9718) covalent geometry : angle 0.57438 (13226) SS BOND : bond 0.00078 ( 2) SS BOND : angle 1.15600 ( 4) hydrogen bonds : bond 0.04407 ( 640) hydrogen bonds : angle 4.01966 ( 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 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.314 Fit side-chains REVERT: A 88 LEU cc_start: 0.8388 (mp) cc_final: 0.8015 (tt) REVERT: A 108 ARG cc_start: 0.7014 (tpp80) cc_final: 0.6650 (tpp80) REVERT: A 396 MET cc_start: 0.6001 (OUTLIER) cc_final: 0.5394 (tmt) REVERT: A 538 ASN cc_start: 0.7934 (t0) cc_final: 0.7596 (m-40) REVERT: A 663 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8164 (mp) REVERT: B 88 LEU cc_start: 0.8396 (mp) cc_final: 0.8025 (tt) REVERT: B 108 ARG cc_start: 0.7018 (tpp80) cc_final: 0.6652 (tpp80) REVERT: B 193 ASP cc_start: 0.8694 (t0) cc_final: 0.8408 (m-30) REVERT: B 396 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5385 (tmt) REVERT: B 538 ASN cc_start: 0.7931 (t0) cc_final: 0.7603 (m-40) REVERT: B 663 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8187 (mp) outliers start: 22 outliers final: 14 residues processed: 138 average time/residue: 0.5730 time to fit residues: 84.8939 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 192 VAL 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 596 LYS Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 VAL 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 596 LYS 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: 0.2980 chunk 94 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.144917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109327 restraints weight = 10543.167| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.74 r_work: 0.3212 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9720 Z= 0.134 Angle : 0.593 9.644 13230 Z= 0.288 Chirality : 0.041 0.130 1494 Planarity : 0.005 0.041 1586 Dihedral : 6.805 52.986 1630 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.07 % Allowed : 17.53 % Favored : 80.39 % 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: 2.04 (0.25), residues: 1194 helix: 2.15 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.65 (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 126 PHE 0.011 0.001 PHE A 614 TRP 0.015 0.001 TRP B 654 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9718) covalent geometry : angle 0.59247 (13226) SS BOND : bond 0.00079 ( 2) SS BOND : angle 1.14744 ( 4) hydrogen bonds : bond 0.04329 ( 640) hydrogen bonds : angle 4.00107 ( 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 143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.400 Fit side-chains REVERT: A 88 LEU cc_start: 0.8427 (mp) cc_final: 0.8071 (tt) REVERT: A 108 ARG cc_start: 0.7070 (tpp80) cc_final: 0.6729 (tpp80) REVERT: A 396 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5477 (tmt) REVERT: A 538 ASN cc_start: 0.7954 (t0) cc_final: 0.7654 (m-40) REVERT: A 663 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8209 (mp) REVERT: B 88 LEU cc_start: 0.8443 (mp) cc_final: 0.8088 (tt) REVERT: B 108 ARG cc_start: 0.7066 (tpp80) cc_final: 0.6720 (tpp80) REVERT: B 396 MET cc_start: 0.6058 (OUTLIER) cc_final: 0.5470 (tmt) REVERT: B 538 ASN cc_start: 0.7975 (t0) cc_final: 0.7690 (m-40) REVERT: B 663 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8229 (mp) outliers start: 20 outliers final: 12 residues processed: 137 average time/residue: 0.5884 time to fit residues: 86.4601 Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 192 VAL 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 148 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 VAL 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: 0.0970 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.143853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.107694 restraints weight = 10506.579| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.74 r_work: 0.3016 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9720 Z= 0.144 Angle : 0.583 9.076 13230 Z= 0.287 Chirality : 0.041 0.132 1494 Planarity : 0.005 0.042 1586 Dihedral : 6.894 54.284 1630 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.07 % Allowed : 17.63 % Favored : 80.29 % 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: 2.13 (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 0.015 0.002 TYR A 126 PHE 0.011 0.001 PHE A 614 TRP 0.014 0.001 TRP B 654 HIS 0.003 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9718) covalent geometry : angle 0.58244 (13226) SS BOND : bond 0.00065 ( 2) SS BOND : angle 1.16640 ( 4) hydrogen bonds : bond 0.04493 ( 640) hydrogen bonds : angle 4.02854 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3339.00 seconds wall clock time: 57 minutes 46.92 seconds (3466.92 seconds total)