Starting phenix.real_space_refine on Sun Jul 27 19:22:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsu_32767/07_2025/7wsu_32767.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsu_32767/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsu_32767/07_2025/7wsu_32767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsu_32767/07_2025/7wsu_32767.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsu_32767/07_2025/7wsu_32767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsu_32767/07_2025/7wsu_32767.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.97, per 1000 atoms: 1.06 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.80 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: 2.71 Time building geometry restraints manager: 2.85 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 45 through 678 or resid 801)) selection = (chain 'B' and (resid 45 through 678 or resid 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: 16.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.050 Find NCS groups from input model: 0.470 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:14.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.220 ------------------------------------------------------------------------------- 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 : 5.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (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 TRP 0.009 0.001 TRP B 45 HIS 0.002 0.001 HIS B 344 PHE 0.008 0.001 PHE A 130 TYR 0.012 0.001 TYR A 594 ARG 0.008 0.001 ARG B 221 Details of bonding type rmsd hydrogen bonds : bond 0.24669 ( 640) hydrogen bonds : angle 7.23651 ( 1890) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.99620 ( 4) covalent geometry : bond 0.00625 ( 9718) covalent geometry : angle 0.73630 (13226) *********************** 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 : 1.089 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 1.1983 time to fit residues: 205.5393 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 : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 0.0570 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.156263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120318 restraints weight = 10322.904| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.94 r_work: 0.3128 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9720 Z= 0.140 Angle : 0.587 6.394 13230 Z= 0.300 Chirality : 0.042 0.142 1494 Planarity : 0.005 0.052 1586 Dihedral : 7.800 58.208 1630 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.66 % Allowed : 9.23 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1194 helix: 1.78 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.69 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 654 HIS 0.002 0.001 HIS B 344 PHE 0.012 0.001 PHE B 579 TYR 0.020 0.002 TYR B 343 ARG 0.003 0.000 ARG B 112 Details of bonding type rmsd hydrogen bonds : bond 0.05471 ( 640) hydrogen bonds : angle 4.57968 ( 1890) SS BOND : bond 0.00096 ( 2) SS BOND : angle 1.03506 ( 4) covalent geometry : bond 0.00293 ( 9718) covalent geometry : angle 0.58683 (13226) *********************** 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 166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.928 Fit side-chains REVERT: A 46 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6022 (mp-120) REVERT: A 108 ARG cc_start: 0.6944 (tpp80) cc_final: 0.6707 (tpp80) REVERT: A 396 MET cc_start: 0.5774 (OUTLIER) cc_final: 0.5016 (tmm) REVERT: A 554 MET cc_start: 0.7859 (mtt) cc_final: 0.7570 (mtp) REVERT: B 46 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6013 (mp-120) REVERT: B 108 ARG cc_start: 0.6943 (tpp80) cc_final: 0.6704 (tpp80) REVERT: B 396 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5001 (tmm) REVERT: B 554 MET cc_start: 0.7879 (mtt) cc_final: 0.7586 (mtp) outliers start: 16 outliers final: 6 residues processed: 158 average time/residue: 1.0466 time to fit residues: 178.7619 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 : 0.959 ------------------------------------------------------------------------------- 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 62 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 19 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 87 optimal weight: 0.0670 chunk 52 optimal weight: 0.4980 chunk 77 optimal weight: 0.3980 chunk 106 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.157062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121403 restraints weight = 10489.913| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.93 r_work: 0.3125 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1898 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= 0.122 Angle : 0.541 6.662 13230 Z= 0.270 Chirality : 0.040 0.131 1494 Planarity : 0.004 0.044 1586 Dihedral : 7.389 57.061 1630 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.59 % Allowed : 10.89 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.25), residues: 1194 helix: 1.98 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.72 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 654 HIS 0.002 0.001 HIS A 344 PHE 0.010 0.001 PHE A 614 TYR 0.018 0.002 TYR B 343 ARG 0.001 0.000 ARG B 587 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 640) hydrogen bonds : angle 4.16503 ( 1890) SS BOND : bond 0.00160 ( 2) SS BOND : angle 1.07246 ( 4) covalent geometry : bond 0.00270 ( 9718) covalent geometry : angle 0.54123 (13226) *********************** 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 161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.946 Fit side-chains REVERT: A 46 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6554 (mp10) REVERT: A 108 ARG cc_start: 0.6940 (tpp80) cc_final: 0.6648 (tpp80) REVERT: A 322 MET cc_start: 0.9210 (tpt) cc_final: 0.8997 (tpt) REVERT: A 396 MET cc_start: 0.5825 (OUTLIER) cc_final: 0.5170 (tmt) REVERT: A 554 MET cc_start: 0.7931 (mtt) cc_final: 0.7723 (mtp) REVERT: B 46 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6540 (mp10) REVERT: B 108 ARG cc_start: 0.6936 (tpp80) cc_final: 0.6642 (tpp80) REVERT: B 322 MET cc_start: 0.9212 (tpt) cc_final: 0.8999 (tpt) REVERT: B 396 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.5177 (tmt) REVERT: B 554 MET cc_start: 0.7944 (mtt) cc_final: 0.7734 (mtp) outliers start: 25 outliers final: 9 residues processed: 146 average time/residue: 1.0358 time to fit residues: 163.4263 Evaluate side-chains 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 311 ASP Chi-restraints excluded: chain A residue 396 MET 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 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 33 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.154660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118214 restraints weight = 10155.960| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.91 r_work: 0.3079 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2038 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= 0.149 Angle : 0.577 7.209 13230 Z= 0.288 Chirality : 0.042 0.181 1494 Planarity : 0.005 0.043 1586 Dihedral : 7.362 57.481 1630 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.80 % Allowed : 12.86 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.25), residues: 1194 helix: 1.98 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.71 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 654 HIS 0.003 0.001 HIS B 344 PHE 0.012 0.001 PHE A 331 TYR 0.016 0.002 TYR A 126 ARG 0.009 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 640) hydrogen bonds : angle 4.11535 ( 1890) SS BOND : bond 0.00094 ( 2) SS BOND : angle 1.22009 ( 4) covalent geometry : bond 0.00349 ( 9718) covalent geometry : angle 0.57633 (13226) *********************** 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 155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.933 Fit side-chains REVERT: A 108 ARG cc_start: 0.6923 (tpp80) cc_final: 0.6644 (tpp80) REVERT: A 193 ASP cc_start: 0.8570 (t0) cc_final: 0.8323 (m-30) REVERT: A 396 MET cc_start: 0.5902 (OUTLIER) cc_final: 0.5276 (tmt) REVERT: A 554 MET cc_start: 0.8006 (mtt) cc_final: 0.7766 (mtp) REVERT: B 108 ARG cc_start: 0.6911 (tpp80) cc_final: 0.6624 (tpp80) REVERT: B 193 ASP cc_start: 0.8560 (t0) cc_final: 0.8315 (m-30) REVERT: B 396 MET cc_start: 0.5909 (OUTLIER) cc_final: 0.5275 (tmt) REVERT: B 554 MET cc_start: 0.7988 (mtt) cc_final: 0.7750 (mtp) outliers start: 27 outliers final: 10 residues processed: 142 average time/residue: 1.1988 time to fit residues: 182.7299 Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 596 LYS 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 596 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.153824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118087 restraints weight = 10188.807| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.84 r_work: 0.3059 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2143 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= 0.138 Angle : 0.558 7.369 13230 Z= 0.278 Chirality : 0.041 0.159 1494 Planarity : 0.005 0.041 1586 Dihedral : 7.132 56.770 1630 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.49 % Allowed : 14.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.25), residues: 1194 helix: 2.04 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.73 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 654 HIS 0.003 0.001 HIS A 344 PHE 0.011 0.001 PHE A 614 TYR 0.015 0.001 TYR A 126 ARG 0.006 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 640) hydrogen bonds : angle 4.04689 ( 1890) SS BOND : bond 0.00100 ( 2) SS BOND : angle 1.19872 ( 4) covalent geometry : bond 0.00321 ( 9718) covalent geometry : angle 0.55794 (13226) *********************** 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 156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.102 Fit side-chains REVERT: A 108 ARG cc_start: 0.7014 (tpp80) cc_final: 0.6685 (tpp80) REVERT: A 193 ASP cc_start: 0.8651 (t0) cc_final: 0.8406 (m-30) REVERT: A 396 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5241 (tmt) REVERT: A 538 ASN cc_start: 0.7953 (t0) cc_final: 0.7576 (m-40) REVERT: A 663 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8110 (mp) REVERT: B 108 ARG cc_start: 0.6954 (tpp80) cc_final: 0.6647 (tpp80) REVERT: B 193 ASP cc_start: 0.8606 (t0) cc_final: 0.8359 (m-30) REVERT: B 396 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5252 (tmt) REVERT: B 663 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8096 (mp) outliers start: 24 outliers final: 10 residues processed: 146 average time/residue: 1.1200 time to fit residues: 175.8434 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 : 0.964 ------------------------------------------------------------------------------- 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 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 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 46 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.143633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.108103 restraints weight = 10524.160| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.75 r_work: 0.3009 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9720 Z= 0.155 Angle : 0.588 8.248 13230 Z= 0.292 Chirality : 0.042 0.135 1494 Planarity : 0.005 0.043 1586 Dihedral : 7.101 56.457 1630 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.70 % Allowed : 15.46 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.25), residues: 1194 helix: 2.02 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.73 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 654 HIS 0.004 0.001 HIS A 344 PHE 0.012 0.001 PHE B 331 TYR 0.016 0.002 TYR B 126 ARG 0.010 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 640) hydrogen bonds : angle 4.06252 ( 1890) SS BOND : bond 0.00055 ( 2) SS BOND : angle 1.23765 ( 4) covalent geometry : bond 0.00370 ( 9718) covalent geometry : angle 0.58747 (13226) *********************** 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 155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.982 Fit side-chains REVERT: A 46 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.5932 (mp-120) REVERT: A 88 LEU cc_start: 0.8395 (mp) cc_final: 0.8006 (tt) REVERT: A 108 ARG cc_start: 0.7000 (tpp80) cc_final: 0.6671 (tpp80) REVERT: A 193 ASP cc_start: 0.8667 (t0) cc_final: 0.8417 (m-30) REVERT: A 396 MET cc_start: 0.5952 (OUTLIER) cc_final: 0.5321 (tmt) REVERT: A 538 ASN cc_start: 0.7959 (t0) cc_final: 0.7602 (m-40) REVERT: A 663 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8112 (mp) REVERT: B 46 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.5907 (mp-120) REVERT: B 88 LEU cc_start: 0.8399 (mp) cc_final: 0.8010 (tt) REVERT: B 108 ARG cc_start: 0.6985 (tpp80) cc_final: 0.6657 (tpp80) REVERT: B 193 ASP cc_start: 0.8647 (t0) cc_final: 0.8390 (m-30) REVERT: B 396 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5315 (tmt) REVERT: B 538 ASN cc_start: 0.7973 (t0) cc_final: 0.7623 (m-40) REVERT: B 663 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8123 (mp) outliers start: 26 outliers final: 10 residues processed: 145 average time/residue: 1.1824 time to fit residues: 184.2144 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 : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN 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 46 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 0.0670 chunk 58 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.145012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108611 restraints weight = 10510.811| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.76 r_work: 0.3024 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2335 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= 0.139 Angle : 0.562 8.188 13230 Z= 0.281 Chirality : 0.041 0.136 1494 Planarity : 0.005 0.042 1586 Dihedral : 6.908 54.611 1630 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.28 % Allowed : 16.80 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1194 helix: 2.09 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.72 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 654 HIS 0.003 0.001 HIS B 344 PHE 0.011 0.001 PHE A 614 TYR 0.015 0.002 TYR B 126 ARG 0.010 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 640) hydrogen bonds : angle 4.04417 ( 1890) SS BOND : bond 0.00082 ( 2) SS BOND : angle 1.18062 ( 4) covalent geometry : bond 0.00325 ( 9718) covalent geometry : angle 0.56174 (13226) *********************** 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 148 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.062 Fit side-chains REVERT: A 46 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.5974 (mp-120) REVERT: A 88 LEU cc_start: 0.8443 (mp) cc_final: 0.8068 (tt) REVERT: A 108 ARG cc_start: 0.7019 (tpp80) cc_final: 0.6667 (tpp80) REVERT: A 193 ASP cc_start: 0.8717 (t0) cc_final: 0.8459 (m-30) REVERT: A 396 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.5398 (tmt) REVERT: A 538 ASN cc_start: 0.7941 (t0) cc_final: 0.7596 (m-40) REVERT: A 663 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8156 (mp) REVERT: B 46 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.5960 (mp-120) REVERT: B 88 LEU cc_start: 0.8442 (mp) cc_final: 0.8070 (tt) REVERT: B 108 ARG cc_start: 0.7015 (tpp80) cc_final: 0.6662 (tpp80) REVERT: B 193 ASP cc_start: 0.8704 (t0) cc_final: 0.8442 (m-30) REVERT: B 396 MET cc_start: 0.6006 (OUTLIER) cc_final: 0.5382 (tmt) REVERT: B 538 ASN cc_start: 0.7961 (t0) cc_final: 0.7625 (m-40) REVERT: B 663 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8157 (mp) outliers start: 22 outliers final: 8 residues processed: 142 average time/residue: 1.1873 time to fit residues: 181.1637 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN 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 46 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.144060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.108618 restraints weight = 10611.774| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.71 r_work: 0.3020 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2381 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= 0.143 Angle : 0.590 9.044 13230 Z= 0.289 Chirality : 0.041 0.131 1494 Planarity : 0.005 0.046 1586 Dihedral : 6.896 53.475 1630 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.28 % Allowed : 17.63 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.25), residues: 1194 helix: 2.07 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.74 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 654 HIS 0.003 0.001 HIS A 344 PHE 0.011 0.001 PHE A 614 TYR 0.015 0.002 TYR A 126 ARG 0.010 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 640) hydrogen bonds : angle 4.05097 ( 1890) SS BOND : bond 0.00068 ( 2) SS BOND : angle 1.19302 ( 4) covalent geometry : bond 0.00337 ( 9718) covalent geometry : angle 0.58992 (13226) *********************** 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 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.940 Fit side-chains REVERT: A 46 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.5966 (mp-120) REVERT: A 88 LEU cc_start: 0.8393 (mp) cc_final: 0.8014 (tt) REVERT: A 108 ARG cc_start: 0.7019 (tpp80) cc_final: 0.6756 (tpp80) REVERT: A 193 ASP cc_start: 0.8678 (t0) cc_final: 0.8394 (m-30) REVERT: A 396 MET cc_start: 0.6001 (OUTLIER) cc_final: 0.5374 (tmt) REVERT: A 538 ASN cc_start: 0.7918 (t0) cc_final: 0.7583 (m-40) REVERT: A 663 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8117 (mp) REVERT: B 46 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.5982 (mp-120) REVERT: B 88 LEU cc_start: 0.8398 (mp) cc_final: 0.8020 (tt) REVERT: B 108 ARG cc_start: 0.7012 (tpp80) cc_final: 0.6646 (tpp80) REVERT: B 193 ASP cc_start: 0.8664 (t0) cc_final: 0.8379 (m-30) REVERT: B 396 MET cc_start: 0.5988 (OUTLIER) cc_final: 0.5369 (tmt) REVERT: B 538 ASN cc_start: 0.7936 (t0) cc_final: 0.7611 (m-40) REVERT: B 663 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8123 (mp) outliers start: 22 outliers final: 8 residues processed: 135 average time/residue: 1.1997 time to fit residues: 173.9897 Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN 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 46 GLN 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 53 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 26 optimal weight: 0.0020 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.143762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108096 restraints weight = 10577.666| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.73 r_work: 0.3013 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2403 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 : 0.576 8.942 13230 Z= 0.285 Chirality : 0.041 0.132 1494 Planarity : 0.005 0.043 1586 Dihedral : 6.914 53.284 1630 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.07 % Allowed : 17.74 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1194 helix: 2.08 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.71 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 654 HIS 0.003 0.001 HIS A 344 PHE 0.011 0.001 PHE A 614 TYR 0.015 0.002 TYR A 126 ARG 0.009 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 640) hydrogen bonds : angle 4.04606 ( 1890) SS BOND : bond 0.00068 ( 2) SS BOND : angle 1.20195 ( 4) covalent geometry : bond 0.00339 ( 9718) covalent geometry : angle 0.57601 (13226) *********************** 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 143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.939 Fit side-chains REVERT: A 46 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6033 (mp-120) REVERT: A 88 LEU cc_start: 0.8365 (mp) cc_final: 0.7993 (tt) REVERT: A 108 ARG cc_start: 0.7027 (tpp80) cc_final: 0.6651 (tpp80) REVERT: A 396 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5393 (tmt) REVERT: A 538 ASN cc_start: 0.7901 (t0) cc_final: 0.7604 (m110) REVERT: A 663 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8129 (mp) REVERT: B 46 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6050 (mp-120) REVERT: B 88 LEU cc_start: 0.8375 (mp) cc_final: 0.8011 (tt) REVERT: B 108 ARG cc_start: 0.7026 (tpp80) cc_final: 0.6649 (tpp80) REVERT: B 396 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5387 (tmt) REVERT: B 538 ASN cc_start: 0.7929 (t0) cc_final: 0.7627 (m110) REVERT: B 663 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8133 (mp) outliers start: 20 outliers final: 8 residues processed: 135 average time/residue: 1.1738 time to fit residues: 170.7080 Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN 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 46 GLN 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 83 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 91 optimal weight: 5.9990 chunk 63 optimal weight: 0.0470 chunk 68 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.145099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110035 restraints weight = 10630.686| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.72 r_work: 0.3215 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2483 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= 0.128 Angle : 0.584 9.581 13230 Z= 0.284 Chirality : 0.040 0.128 1494 Planarity : 0.005 0.042 1586 Dihedral : 6.806 53.423 1630 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.56 % Allowed : 18.26 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.25), residues: 1194 helix: 2.12 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.63 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 654 HIS 0.002 0.001 HIS B 344 PHE 0.011 0.001 PHE A 614 TYR 0.014 0.002 TYR B 126 ARG 0.009 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 640) hydrogen bonds : angle 4.00439 ( 1890) SS BOND : bond 0.00074 ( 2) SS BOND : angle 1.17600 ( 4) covalent geometry : bond 0.00291 ( 9718) covalent geometry : angle 0.58379 (13226) ********************** 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 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.035 Fit side-chains REVERT: A 46 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6097 (mp-120) REVERT: A 88 LEU cc_start: 0.8416 (mp) cc_final: 0.8058 (tt) REVERT: A 108 ARG cc_start: 0.7072 (tpp80) cc_final: 0.6715 (tpp80) REVERT: A 396 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5463 (tmt) REVERT: A 538 ASN cc_start: 0.7885 (t0) cc_final: 0.7619 (m110) REVERT: A 663 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8175 (mp) REVERT: B 46 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6106 (mp-120) REVERT: B 88 LEU cc_start: 0.8429 (mp) cc_final: 0.8072 (tt) REVERT: B 108 ARG cc_start: 0.7080 (tpp80) cc_final: 0.6721 (tpp80) REVERT: B 396 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5449 (tmt) REVERT: B 538 ASN cc_start: 0.7926 (t0) cc_final: 0.7659 (m110) REVERT: B 663 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8174 (mp) outliers start: 15 outliers final: 7 residues processed: 134 average time/residue: 1.1989 time to fit residues: 172.4983 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN 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 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 663 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 114 optimal weight: 0.0770 chunk 68 optimal weight: 0.0770 chunk 86 optimal weight: 0.0000 chunk 103 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 0.0020 overall best weight: 0.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.147929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.112560 restraints weight = 10525.304| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.73 r_work: 0.3258 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9720 Z= 0.113 Angle : 0.552 9.100 13230 Z= 0.270 Chirality : 0.039 0.123 1494 Planarity : 0.004 0.041 1586 Dihedral : 6.547 52.105 1630 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.14 % Allowed : 19.09 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.25), residues: 1194 helix: 2.27 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.63 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 654 HIS 0.001 0.000 HIS A 344 PHE 0.010 0.001 PHE A 614 TYR 0.012 0.001 TYR A 126 ARG 0.009 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 640) hydrogen bonds : angle 3.90890 ( 1890) SS BOND : bond 0.00090 ( 2) SS BOND : angle 1.15083 ( 4) covalent geometry : bond 0.00242 ( 9718) covalent geometry : angle 0.55167 (13226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6914.84 seconds wall clock time: 118 minutes 51.25 seconds (7131.25 seconds total)