Starting phenix.real_space_refine on Wed Aug 5 11:37:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/31ey_58353/08_2026/31ey_58353.cif Found real_map, /net/cci-nas-00/data/ceres_data/31ey_58353/08_2026/31ey_58353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/31ey_58353/08_2026/31ey_58353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/31ey_58353/08_2026/31ey_58353.map" model { file = "/net/cci-nas-00/data/ceres_data/31ey_58353/08_2026/31ey_58353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/31ey_58353/08_2026/31ey_58353.cif" } resolution = 2.59 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= 0.014 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6294 2.51 5 N 1246 2.21 5 O 1724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3873 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 486} Chain: "B" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3873 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 486} Chain: "A" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 747 Unusual residues: {'DAO': 6, 'ERG': 4, 'FAW': 2, 'LMT': 7, 'MYR': 11, 'PLM': 3} Classifications: {'undetermined': 33} Link IDs: {None: 32} Chain: "B" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 747 Unusual residues: {'DAO': 6, 'ERG': 4, 'FAW': 2, 'LMT': 7, 'MYR': 11, 'PLM': 3} Classifications: {'undetermined': 33} Link IDs: {None: 32} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Time building chain proxies: 2.16, per 1000 atoms: 0.23 Number of scatterers: 9336 At special positions: 0 Unit cell: (89.5607, 113.712, 78.4914, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1724 8.00 N 1246 7.00 C 6294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 185 " distance=2.03 Simple disulfide: pdb=" SG CYS B 248 " - pdb=" SG CYS B 255 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 335.3 milliseconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 73.0% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 28 through 37 removed outlier: 3.899A pdb=" N ALA A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 75 through 105 removed outlier: 4.611A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLY A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 108 through 133 removed outlier: 3.569A pdb=" N VAL A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 removed outlier: 3.946A pdb=" N ILE A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.958A pdb=" N TYR A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.516A pdb=" N ILE A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 243 Proline residue: A 225 - end of helix removed outlier: 3.973A pdb=" N GLY A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N THR A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 289 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.840A pdb=" N SER A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 Processing helix chain 'A' and resid 316 through 323 removed outlier: 4.113A pdb=" N ILE A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 342 through 368 Processing helix chain 'A' and resid 374 through 398 removed outlier: 3.712A pdb=" N VAL A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.710A pdb=" N VAL A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 437 Processing helix chain 'A' and resid 437 through 446 removed outlier: 4.206A pdb=" N ALA A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 473 removed outlier: 3.580A pdb=" N MET A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 495 removed outlier: 3.845A pdb=" N THR A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 513 through 526 Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.761A pdb=" N VAL A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.801A pdb=" N THR B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 51 removed outlier: 4.359A pdb=" N LEU B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 51' Processing helix chain 'B' and resid 75 through 105 removed outlier: 4.650A pdb=" N ALA B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Proline residue: B 97 - end of helix removed outlier: 3.522A pdb=" N LEU B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 133 removed outlier: 3.580A pdb=" N VAL B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 171 removed outlier: 3.949A pdb=" N ILE B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 removed outlier: 4.004A pdb=" N TYR B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.512A pdb=" N ILE B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 243 Proline residue: B 225 - end of helix removed outlier: 3.955A pdb=" N GLY B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 289 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.827A pdb=" N SER B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 316 through 322 removed outlier: 4.083A pdb=" N ILE B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 342 through 368 Processing helix chain 'B' and resid 374 through 398 removed outlier: 3.720A pdb=" N VAL B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 417 removed outlier: 3.815A pdb=" N VAL B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 437 Processing helix chain 'B' and resid 437 through 446 removed outlier: 4.218A pdb=" N ALA B 441 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 473 removed outlier: 3.589A pdb=" N MET B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 removed outlier: 3.835A pdb=" N THR B 495 " --> pdb=" O GLY B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 513 through 526 Processing helix chain 'B' and resid 526 through 542 removed outlier: 3.748A pdb=" N VAL B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA3, first strand: chain 'A' and resid 254 through 255 removed outlier: 3.516A pdb=" N LEU A 264 " --> pdb=" O CYS A 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.530A pdb=" N LEU B 264 " --> pdb=" O CYS B 255 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1527 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: 1.46 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1405 1.33 - 1.45: 2216 1.45 - 1.57: 5691 1.57 - 1.69: 0 1.69 - 1.81: 106 Bond restraints: 9418 Sorted by residual: bond pdb=" C VAL A 372 " pdb=" O VAL A 372 " ideal model delta sigma weight residual 1.242 1.226 0.017 1.23e-02 6.61e+03 1.86e+00 bond pdb=" C VAL B 372 " pdb=" O VAL B 372 " ideal model delta sigma weight residual 1.242 1.226 0.017 1.23e-02 6.61e+03 1.80e+00 bond pdb=" CB GLU B 178 " pdb=" CG GLU B 178 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB ARG A 38 " pdb=" CG ARG A 38 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" C THR B 401 " pdb=" N PRO B 402 " ideal model delta sigma weight residual 1.332 1.345 -0.013 1.30e-02 5.92e+03 1.01e+00 ... (remaining 9413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 12359 1.78 - 3.57: 219 3.57 - 5.35: 18 5.35 - 7.14: 8 7.14 - 8.92: 4 Bond angle restraints: 12608 Sorted by residual: angle pdb=" CA GLU B 178 " pdb=" CB GLU B 178 " pdb=" CG GLU B 178 " ideal model delta sigma weight residual 114.10 120.64 -6.54 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CA ARG A 38 " pdb=" CB ARG A 38 " pdb=" CG ARG A 38 " ideal model delta sigma weight residual 114.10 120.35 -6.25 2.00e+00 2.50e-01 9.75e+00 angle pdb=" C1B LMT A 625 " pdb=" O1B LMT A 625 " pdb=" C4' LMT A 625 " ideal model delta sigma weight residual 117.87 126.79 -8.92 3.00e+00 1.11e-01 8.84e+00 angle pdb=" C1B LMT B 627 " pdb=" O1B LMT B 627 " pdb=" C4' LMT B 627 " ideal model delta sigma weight residual 117.87 126.73 -8.86 3.00e+00 1.11e-01 8.72e+00 angle pdb=" CB GLU B 178 " pdb=" CG GLU B 178 " pdb=" CD GLU B 178 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.70e+00 3.46e-01 7.73e+00 ... (remaining 12603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 6250 21.52 - 43.04: 347 43.04 - 64.56: 71 64.56 - 86.09: 18 86.09 - 107.61: 4 Dihedral angle restraints: 6690 sinusoidal: 3732 harmonic: 2958 Sorted by residual: dihedral pdb=" CB3 FAW A 606 " pdb=" CB1 FAW A 606 " pdb=" CB2 FAW A 606 " pdb=" OG2 FAW A 606 " ideal model delta sinusoidal sigma weight residual 167.11 -85.28 -107.61 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" CB3 FAW B 608 " pdb=" CB1 FAW B 608 " pdb=" CB2 FAW B 608 " pdb=" OG2 FAW B 608 " ideal model delta sinusoidal sigma weight residual 167.11 -87.65 -105.24 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" CA ASP B 319 " pdb=" CB ASP B 319 " pdb=" CG ASP B 319 " pdb=" OD1 ASP B 319 " ideal model delta sinusoidal sigma weight residual -30.00 -88.92 58.92 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 6687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1419 0.080 - 0.159: 79 0.159 - 0.239: 0 0.239 - 0.319: 0 0.319 - 0.398: 2 Chirality restraints: 1500 Sorted by residual: chirality pdb=" C1B LMT A 625 " pdb=" C2B LMT A 625 " pdb=" O1B LMT A 625 " pdb=" O5B LMT A 625 " both_signs ideal model delta sigma weight residual False -2.20 -1.80 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" C1B LMT B 627 " pdb=" C2B LMT B 627 " pdb=" O1B LMT B 627 " pdb=" O5B LMT B 627 " both_signs ideal model delta sigma weight residual False -2.20 -1.81 -0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" C2B LMT A 625 " pdb=" C1B LMT A 625 " pdb=" C3B LMT A 625 " pdb=" O2B LMT A 625 " both_signs ideal model delta sigma weight residual False -2.44 -2.29 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 1497 not shown) Planarity restraints: 1420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 340 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO A 341 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 340 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO B 341 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 341 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 341 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 447 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 448 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 448 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 448 " 0.026 5.00e-02 4.00e+02 ... (remaining 1417 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.98: 4256 2.98 - 3.46: 8888 3.46 - 3.94: 15046 3.94 - 4.42: 18180 4.42 - 4.90: 28333 Nonbonded interactions: 74703 Sorted by model distance: nonbonded pdb=" N GLU B 178 " pdb=" OE1 GLU B 178 " model vdw 2.494 3.120 nonbonded pdb=" OD2 ASP A 360 " pdb=" O PHE A 406 " model vdw 2.527 3.040 nonbonded pdb=" O1B LMT B 627 " pdb=" O2B LMT B 627 " model vdw 2.537 2.432 nonbonded pdb=" O1B LMT A 625 " pdb=" O2B LMT A 625 " model vdw 2.539 2.432 nonbonded pdb=" OD2 ASP B 360 " pdb=" O PHE B 406 " model vdw 2.544 3.040 ... (remaining 74698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 601 or resid 609 or resid 611 or resid 613 thro \ ugh 614 or resid 623 or resid 629 through 630)) selection = (chain 'B' and (resid 28 through 601 or resid 609 or resid 611 or resid 613 thro \ ugh 614 or resid 623 or resid 629 through 630)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.050 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 0.003 0.038 9422 Z= 0.136 Angle : 0.597 8.919 12616 Z= 0.312 Chirality : 0.040 0.398 1500 Planarity : 0.005 0.051 1420 Dihedral : 13.548 107.607 4782 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.68 % Favored : 99.13 % Rotamer: Outliers : 0.24 % Allowed : 7.57 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.93 (0.25), residues: 1036 helix: 1.93 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -0.05 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.008 0.001 TYR A 339 PHE 0.021 0.001 PHE A 406 TRP 0.007 0.001 TRP A 266 HIS 0.009 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 9418) covalent geometry : angle 0.59705 / 0.31 (12608) SS BOND : bond 0.00177 / 0.08 ( 4) SS BOND : angle 0.41415 / 0.23 ( 8) hydrogen bonds : bond 0.11825 / 7.54 ( 515) hydrogen bonds : angle 4.53415 / 3.26 ( 1527) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8965 (mtm) cc_final: 0.8517 (mtm) REVERT: A 511 ARG cc_start: 0.7445 (mmm160) cc_final: 0.7231 (mmm160) REVERT: B 138 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8228 (mtmm) REVERT: B 253 MET cc_start: 0.8990 (mtm) cc_final: 0.8695 (mtp) outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 0.8260 time to fit residues: 58.3145 Evaluate side-chains 64 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.125373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097530 restraints weight = 12766.141| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.98 r_work: 0.3156 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9422 Z= 0.120 Angle : 0.526 9.013 12616 Z= 0.250 Chirality : 0.041 0.446 1500 Planarity : 0.005 0.050 1420 Dihedral : 10.225 102.699 3097 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.77 % Favored : 99.03 % Rotamer: Outliers : 1.08 % Allowed : 7.45 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.19 (0.25), residues: 1036 helix: 2.12 (0.19), residues: 706 sheet: None (None), residues: 0 loop : 0.03 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 262 TYR 0.009 0.001 TYR B 492 PHE 0.014 0.001 PHE B 528 TRP 0.013 0.001 TRP B 242 HIS 0.002 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9418) covalent geometry : angle 0.52641 / 0.25 (12608) SS BOND : bond 0.00191 / 0.09 ( 4) SS BOND : angle 0.43712 / 0.25 ( 8) hydrogen bonds : bond 0.04948 / 3.41 ( 515) hydrogen bonds : angle 3.78458 / 2.71 ( 1527) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 360 ASP cc_start: 0.8251 (t70) cc_final: 0.7936 (t70) REVERT: A 511 ARG cc_start: 0.7451 (mmm160) cc_final: 0.7250 (mmm160) REVERT: B 138 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8099 (mmtp) REVERT: B 216 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8036 (ttmm) REVERT: B 253 MET cc_start: 0.8895 (mtm) cc_final: 0.8551 (mtm) REVERT: B 360 ASP cc_start: 0.8310 (t70) cc_final: 0.7992 (t70) outliers start: 9 outliers final: 3 residues processed: 76 average time/residue: 0.7780 time to fit residues: 62.5773 Evaluate side-chains 69 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.094818 restraints weight = 12897.075| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.04 r_work: 0.3082 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9422 Z= 0.137 Angle : 0.530 7.968 12616 Z= 0.254 Chirality : 0.040 0.388 1500 Planarity : 0.005 0.050 1420 Dihedral : 10.091 97.508 3094 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.87 % Favored : 98.94 % Rotamer: Outliers : 1.44 % Allowed : 7.69 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.19 (0.25), residues: 1036 helix: 2.17 (0.19), residues: 698 sheet: None (None), residues: 0 loop : -0.02 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 369 TYR 0.013 0.001 TYR B 137 PHE 0.015 0.001 PHE B 528 TRP 0.011 0.001 TRP B 242 HIS 0.001 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9418) covalent geometry : angle 0.52960 / 0.25 (12608) SS BOND : bond 0.00272 / 0.13 ( 4) SS BOND : angle 0.42410 / 0.23 ( 8) hydrogen bonds : bond 0.05525 / 3.80 ( 515) hydrogen bonds : angle 3.82457 / 2.74 ( 1527) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8591 (mp10) cc_final: 0.8253 (mp10) REVERT: A 216 LYS cc_start: 0.8288 (ttmt) cc_final: 0.8029 (ttmm) REVERT: A 253 MET cc_start: 0.9023 (mtm) cc_final: 0.8744 (mtp) REVERT: B 44 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8029 (t0) REVERT: B 137 TYR cc_start: 0.8307 (t80) cc_final: 0.7903 (t80) REVERT: B 216 LYS cc_start: 0.8363 (ttmt) cc_final: 0.8087 (ttmm) outliers start: 12 outliers final: 4 residues processed: 74 average time/residue: 0.8073 time to fit residues: 63.1259 Evaluate side-chains 69 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.093024 restraints weight = 13091.119| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.08 r_work: 0.3115 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9422 Z= 0.139 Angle : 0.520 7.164 12616 Z= 0.251 Chirality : 0.040 0.348 1500 Planarity : 0.005 0.050 1420 Dihedral : 10.066 93.106 3094 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.77 % Favored : 99.03 % Rotamer: Outliers : 1.68 % Allowed : 8.17 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.23 (0.25), residues: 1036 helix: 2.19 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 0.00 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.019 0.001 TYR B 137 PHE 0.015 0.001 PHE B 528 TRP 0.010 0.001 TRP B 242 HIS 0.001 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9418) covalent geometry : angle 0.52049 / 0.25 (12608) SS BOND : bond 0.00228 / 0.10 ( 4) SS BOND : angle 0.37764 / 0.20 ( 8) hydrogen bonds : bond 0.05447 / 3.75 ( 515) hydrogen bonds : angle 3.79502 / 2.72 ( 1527) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8631 (mp10) cc_final: 0.8282 (mp10) REVERT: A 216 LYS cc_start: 0.8273 (ttmt) cc_final: 0.8014 (ttmm) REVERT: A 253 MET cc_start: 0.9016 (mtm) cc_final: 0.8767 (mtp) REVERT: A 406 PHE cc_start: 0.8319 (t80) cc_final: 0.8091 (t80) REVERT: B 44 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8019 (t0) REVERT: B 137 TYR cc_start: 0.8090 (t80) cc_final: 0.7725 (t80) REVERT: B 216 LYS cc_start: 0.8335 (ttmt) cc_final: 0.8044 (ttmm) outliers start: 14 outliers final: 7 residues processed: 74 average time/residue: 0.7902 time to fit residues: 61.8702 Evaluate side-chains 73 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.088342 restraints weight = 12396.977| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.93 r_work: 0.2914 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9422 Z= 0.134 Angle : 0.508 6.549 12616 Z= 0.246 Chirality : 0.039 0.321 1500 Planarity : 0.005 0.050 1420 Dihedral : 9.953 89.127 3094 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.87 % Favored : 98.94 % Rotamer: Outliers : 1.44 % Allowed : 9.13 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.26 (0.25), residues: 1036 helix: 2.21 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 0.03 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 373 TYR 0.016 0.001 TYR B 137 PHE 0.014 0.001 PHE B 528 TRP 0.009 0.001 TRP B 242 HIS 0.001 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 9418) covalent geometry : angle 0.50789 / 0.25 (12608) SS BOND : bond 0.00228 / 0.11 ( 4) SS BOND : angle 0.35866 / 0.20 ( 8) hydrogen bonds : bond 0.05333 / 3.67 ( 515) hydrogen bonds : angle 3.75331 / 2.68 ( 1527) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8741 (mp10) cc_final: 0.8417 (mp10) REVERT: A 216 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8270 (ttmm) REVERT: B 44 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8055 (t0) REVERT: B 137 TYR cc_start: 0.8208 (t80) cc_final: 0.7805 (t80) REVERT: B 175 GLN cc_start: 0.8722 (mp10) cc_final: 0.8279 (mp10) REVERT: B 216 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8242 (ttmm) outliers start: 12 outliers final: 7 residues processed: 73 average time/residue: 0.7538 time to fit residues: 58.2489 Evaluate side-chains 70 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 15 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 54 optimal weight: 0.0370 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.090301 restraints weight = 12399.172| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.94 r_work: 0.2968 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9422 Z= 0.106 Angle : 0.469 6.339 12616 Z= 0.228 Chirality : 0.037 0.313 1500 Planarity : 0.005 0.049 1420 Dihedral : 9.456 87.174 3094 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.87 % Favored : 98.94 % Rotamer: Outliers : 1.56 % Allowed : 9.13 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.57 (0.25), residues: 1036 helix: 2.40 (0.19), residues: 706 sheet: None (None), residues: 0 loop : 0.19 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 373 TYR 0.015 0.001 TYR B 137 PHE 0.014 0.001 PHE B 406 TRP 0.008 0.001 TRP B 242 HIS 0.001 0.000 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 9418) covalent geometry : angle 0.46908 / 0.23 (12608) SS BOND : bond 0.00159 / 0.07 ( 4) SS BOND : angle 0.25239 / 0.14 ( 8) hydrogen bonds : bond 0.04436 / 3.05 ( 515) hydrogen bonds : angle 3.59329 / 2.57 ( 1527) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.284 Fit side-chains REVERT: A 175 GLN cc_start: 0.8756 (mp10) cc_final: 0.8437 (mp10) REVERT: A 216 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8312 (ttmm) REVERT: A 400 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8801 (tpp) REVERT: B 44 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8051 (t70) REVERT: B 137 TYR cc_start: 0.8159 (t80) cc_final: 0.7732 (t80) REVERT: B 216 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8255 (ttmm) REVERT: B 511 ARG cc_start: 0.7906 (mmm160) cc_final: 0.7665 (mmp-170) outliers start: 13 outliers final: 6 residues processed: 79 average time/residue: 0.7460 time to fit residues: 62.2334 Evaluate side-chains 72 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 98 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 100 optimal weight: 0.0470 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090397 restraints weight = 12499.038| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.94 r_work: 0.2952 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9422 Z= 0.115 Angle : 0.477 6.191 12616 Z= 0.232 Chirality : 0.038 0.308 1500 Planarity : 0.005 0.049 1420 Dihedral : 9.492 84.297 3094 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.97 % Favored : 98.84 % Rotamer: Outliers : 1.20 % Allowed : 9.50 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.58 (0.25), residues: 1036 helix: 2.46 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 0.15 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 373 TYR 0.016 0.001 TYR B 137 PHE 0.020 0.001 PHE B 406 TRP 0.008 0.001 TRP B 242 HIS 0.001 0.000 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9418) covalent geometry : angle 0.47704 / 0.23 (12608) SS BOND : bond 0.00187 / 0.09 ( 4) SS BOND : angle 0.30579 / 0.17 ( 8) hydrogen bonds : bond 0.04798 / 3.30 ( 515) hydrogen bonds : angle 3.61903 / 2.59 ( 1527) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.322 Fit side-chains REVERT: A 175 GLN cc_start: 0.8807 (mp10) cc_final: 0.8502 (mp10) REVERT: A 216 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8304 (ttmm) REVERT: A 400 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8806 (tpp) REVERT: B 44 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8033 (t0) REVERT: B 137 TYR cc_start: 0.8171 (t80) cc_final: 0.7733 (t80) REVERT: B 138 LYS cc_start: 0.8439 (mmtp) cc_final: 0.8162 (mmtt) REVERT: B 216 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8256 (ttmm) REVERT: B 511 ARG cc_start: 0.7931 (mmm160) cc_final: 0.7682 (mmp-170) outliers start: 10 outliers final: 6 residues processed: 71 average time/residue: 0.7410 time to fit residues: 55.5837 Evaluate side-chains 72 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 0.7980 chunk 100 optimal weight: 0.0050 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 0.0020 chunk 75 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.120001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.092069 restraints weight = 12373.878| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.94 r_work: 0.2983 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9422 Z= 0.103 Angle : 0.461 6.099 12616 Z= 0.224 Chirality : 0.037 0.304 1500 Planarity : 0.005 0.048 1420 Dihedral : 9.254 81.984 3094 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.87 % Favored : 98.94 % Rotamer: Outliers : 1.20 % Allowed : 10.34 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.76 (0.25), residues: 1036 helix: 2.53 (0.19), residues: 706 sheet: None (None), residues: 0 loop : 0.32 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 373 TYR 0.015 0.001 TYR B 137 PHE 0.022 0.001 PHE B 406 TRP 0.007 0.001 TRP B 242 HIS 0.001 0.000 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9418) covalent geometry : angle 0.46142 / 0.22 (12608) SS BOND : bond 0.00117 / 0.06 ( 4) SS BOND : angle 0.26103 / 0.15 ( 8) hydrogen bonds : bond 0.04306 / 2.95 ( 515) hydrogen bonds : angle 3.52603 / 2.52 ( 1527) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8815 (mp10) cc_final: 0.8510 (mp10) REVERT: A 216 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8299 (ttmm) REVERT: A 400 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8773 (tpp) REVERT: B 44 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8046 (t70) REVERT: B 216 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8276 (ttmm) outliers start: 10 outliers final: 4 residues processed: 73 average time/residue: 0.7598 time to fit residues: 58.7787 Evaluate side-chains 69 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.088140 restraints weight = 12357.629| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.96 r_work: 0.2944 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9422 Z= 0.117 Angle : 0.480 5.994 12616 Z= 0.234 Chirality : 0.038 0.300 1500 Planarity : 0.005 0.048 1420 Dihedral : 9.361 79.041 3094 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.97 % Favored : 98.84 % Rotamer: Outliers : 0.84 % Allowed : 10.94 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.66 (0.25), residues: 1036 helix: 2.51 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 0.19 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 511 TYR 0.016 0.001 TYR B 137 PHE 0.026 0.001 PHE B 406 TRP 0.007 0.001 TRP B 242 HIS 0.001 0.000 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9418) covalent geometry : angle 0.47966 / 0.23 (12608) SS BOND : bond 0.00187 / 0.09 ( 4) SS BOND : angle 0.32380 / 0.18 ( 8) hydrogen bonds : bond 0.04859 / 3.34 ( 515) hydrogen bonds : angle 3.61486 / 2.58 ( 1527) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8811 (mp10) cc_final: 0.8494 (mp10) REVERT: A 216 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8203 (ttmm) REVERT: A 400 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8718 (tpp) REVERT: B 44 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8065 (t0) REVERT: B 216 LYS cc_start: 0.8437 (ttmt) cc_final: 0.8119 (ttmm) outliers start: 7 outliers final: 5 residues processed: 70 average time/residue: 0.7521 time to fit residues: 55.5719 Evaluate side-chains 71 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 4 optimal weight: 0.0010 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.091924 restraints weight = 12376.075| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.93 r_work: 0.3017 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9422 Z= 0.106 Angle : 0.468 6.170 12616 Z= 0.229 Chirality : 0.037 0.299 1500 Planarity : 0.005 0.048 1420 Dihedral : 9.012 77.153 3094 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.87 % Favored : 98.94 % Rotamer: Outliers : 0.96 % Allowed : 11.30 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.79 (0.25), residues: 1036 helix: 2.56 (0.19), residues: 706 sheet: None (None), residues: 0 loop : 0.30 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 373 TYR 0.015 0.001 TYR B 137 PHE 0.028 0.001 PHE B 406 TRP 0.007 0.001 TRP B 242 HIS 0.001 0.000 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 9418) covalent geometry : angle 0.46783 / 0.23 (12608) SS BOND : bond 0.00160 / 0.07 ( 4) SS BOND : angle 0.28937 / 0.16 ( 8) hydrogen bonds : bond 0.04350 / 2.99 ( 515) hydrogen bonds : angle 3.53410 / 2.53 ( 1527) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8881 (mp10) cc_final: 0.8537 (mp10) REVERT: A 216 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8279 (ttmm) REVERT: A 360 ASP cc_start: 0.8589 (t70) cc_final: 0.8357 (t0) REVERT: A 400 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8765 (tpp) REVERT: B 44 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8043 (t70) REVERT: B 216 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8238 (ttmm) outliers start: 8 outliers final: 5 residues processed: 72 average time/residue: 0.6697 time to fit residues: 51.1345 Evaluate side-chains 71 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.089779 restraints weight = 12230.022| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.92 r_work: 0.2985 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9422 Z= 0.119 Angle : 0.485 6.327 12616 Z= 0.238 Chirality : 0.038 0.295 1500 Planarity : 0.005 0.048 1420 Dihedral : 9.179 74.884 3094 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.97 % Favored : 98.84 % Rotamer: Outliers : 0.96 % Allowed : 11.30 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.68 (0.25), residues: 1036 helix: 2.52 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 0.20 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 133 TYR 0.014 0.001 TYR B 137 PHE 0.034 0.001 PHE B 406 TRP 0.007 0.001 TRP B 242 HIS 0.002 0.000 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9418) covalent geometry : angle 0.48554 / 0.24 (12608) SS BOND : bond 0.00217 / 0.10 ( 4) SS BOND : angle 0.33476 / 0.18 ( 8) hydrogen bonds : bond 0.04906 / 3.37 ( 515) hydrogen bonds : angle 3.63402 / 2.60 ( 1527) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2852.56 seconds wall clock time: 49 minutes 29.90 seconds (2969.90 seconds total)