Starting phenix.real_space_refine on Sat Oct 11 17:32:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wzj_37954/10_2025/8wzj_37954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wzj_37954/10_2025/8wzj_37954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wzj_37954/10_2025/8wzj_37954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wzj_37954/10_2025/8wzj_37954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wzj_37954/10_2025/8wzj_37954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wzj_37954/10_2025/8wzj_37954.map" } resolution = 2.7 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= 0.000 sd= 0.012 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10392 2.51 5 N 2884 2.21 5 O 3024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16368 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: A, C, D Time building chain proxies: 3.53, per 1000 atoms: 0.22 Number of scatterers: 16368 At special positions: 0 Unit cell: (108.07, 114.49, 84.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 12 15.00 O 3024 8.00 N 2884 7.00 C 10392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 657.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3712 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 39.0% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 202 through 205 removed outlier: 3.657A pdb=" N ILE B 205 " --> pdb=" O ASP B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 246 through 257 removed outlier: 3.893A pdb=" N GLN B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 366 removed outlier: 3.915A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.650A pdb=" N LEU B 419 " --> pdb=" O PRO B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 471 through 486 Processing helix chain 'B' and resid 486 through 501 Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 202 through 205 removed outlier: 3.657A pdb=" N ILE A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.894A pdb=" N GLN A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.914A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.649A pdb=" N LEU A 419 " --> pdb=" O PRO A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 471 through 486 Processing helix chain 'A' and resid 486 through 501 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 202 through 205 removed outlier: 3.658A pdb=" N ILE C 205 " --> pdb=" O ASP C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.894A pdb=" N GLN C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 348 through 366 removed outlier: 3.914A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.650A pdb=" N LEU C 419 " --> pdb=" O PRO C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 486 through 501 Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 54 through 65 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 160 through 169 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'D' and resid 202 through 205 removed outlier: 3.658A pdb=" N ILE D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 202 through 205' Processing helix chain 'D' and resid 246 through 257 removed outlier: 3.894A pdb=" N GLN D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 272 Processing helix chain 'D' and resid 285 through 291 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 348 through 366 removed outlier: 3.914A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) Proline residue: D 359 - end of helix Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 415 through 419 removed outlier: 3.650A pdb=" N LEU D 419 " --> pdb=" O PRO D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 450 Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 486 through 501 Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=AA2, first strand: chain 'B' and resid 343 through 345 removed outlier: 5.988A pdb=" N ILE B 281 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 429 through 431 Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 5.987A pdb=" N ILE A 281 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 345 removed outlier: 5.987A pdb=" N ILE C 281 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 345 removed outlier: 5.988A pdb=" N ILE D 281 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1872 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: 2.72 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 6777 1.39 - 1.57: 9987 1.57 - 1.75: 20 1.75 - 1.93: 92 1.93 - 2.11: 12 Bond restraints: 16888 Sorted by residual: bond pdb=" O2B NDP D3002 " pdb=" P2B NDP D3002 " ideal model delta sigma weight residual 1.833 1.621 0.212 3.80e-02 6.93e+02 3.10e+01 bond pdb=" O2B NDP B3002 " pdb=" P2B NDP B3002 " ideal model delta sigma weight residual 1.833 1.622 0.211 3.80e-02 6.93e+02 3.09e+01 bond pdb=" O2B NDP C3002 " pdb=" P2B NDP C3002 " ideal model delta sigma weight residual 1.833 1.622 0.211 3.80e-02 6.93e+02 3.09e+01 bond pdb=" O2B NDP A3002 " pdb=" P2B NDP A3002 " ideal model delta sigma weight residual 1.833 1.622 0.211 3.80e-02 6.93e+02 3.08e+01 bond pdb=" O5D NDP A3002 " pdb=" PN NDP A3002 " ideal model delta sigma weight residual 1.757 1.602 0.155 3.50e-02 8.16e+02 1.95e+01 ... (remaining 16883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.73: 22912 4.73 - 9.45: 104 9.45 - 14.18: 12 14.18 - 18.91: 8 18.91 - 23.63: 4 Bond angle restraints: 23040 Sorted by residual: angle pdb=" PA NDP C3002 " pdb=" O3 NDP C3002 " pdb=" PN NDP C3002 " ideal model delta sigma weight residual 107.74 131.37 -23.63 1.95e+00 2.62e-01 1.46e+02 angle pdb=" PA NDP D3002 " pdb=" O3 NDP D3002 " pdb=" PN NDP D3002 " ideal model delta sigma weight residual 107.74 131.36 -23.62 1.95e+00 2.62e-01 1.46e+02 angle pdb=" PA NDP A3002 " pdb=" O3 NDP A3002 " pdb=" PN NDP A3002 " ideal model delta sigma weight residual 107.74 131.33 -23.59 1.95e+00 2.62e-01 1.46e+02 angle pdb=" PA NDP B3002 " pdb=" O3 NDP B3002 " pdb=" PN NDP B3002 " ideal model delta sigma weight residual 107.74 131.33 -23.59 1.95e+00 2.62e-01 1.46e+02 angle pdb=" C5B NDP C3002 " pdb=" O5B NDP C3002 " pdb=" PA NDP C3002 " ideal model delta sigma weight residual 103.84 120.50 -16.66 1.91e+00 2.73e-01 7.57e+01 ... (remaining 23035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.88: 9054 18.88 - 37.76: 622 37.76 - 56.64: 124 56.64 - 75.52: 48 75.52 - 94.40: 12 Dihedral angle restraints: 9860 sinusoidal: 4080 harmonic: 5780 Sorted by residual: dihedral pdb=" CA ASP C 389 " pdb=" C ASP C 389 " pdb=" N GLY C 390 " pdb=" CA GLY C 390 " ideal model delta harmonic sigma weight residual 180.00 158.93 21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ASP D 389 " pdb=" C ASP D 389 " pdb=" N GLY D 390 " pdb=" CA GLY D 390 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ASP A 389 " pdb=" C ASP A 389 " pdb=" N GLY A 390 " pdb=" CA GLY A 390 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 9857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 932 0.045 - 0.090: 777 0.090 - 0.136: 466 0.136 - 0.181: 142 0.181 - 0.226: 11 Chirality restraints: 2328 Sorted by residual: chirality pdb=" C4D NDP C3002 " pdb=" C3D NDP C3002 " pdb=" C5D NDP C3002 " pdb=" O4D NDP C3002 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C4D NDP B3002 " pdb=" C3D NDP B3002 " pdb=" C5D NDP B3002 " pdb=" O4D NDP B3002 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C4D NDP A3002 " pdb=" C3D NDP A3002 " pdb=" C5D NDP A3002 " pdb=" O4D NDP A3002 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2325 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A3002 " -0.054 2.00e-02 2.50e+03 3.42e-02 1.46e+01 pdb=" C3N NDP A3002 " -0.012 2.00e-02 2.50e+03 pdb=" C4N NDP A3002 " -0.007 2.00e-02 2.50e+03 pdb=" C7N NDP A3002 " 0.030 2.00e-02 2.50e+03 pdb=" N1N NDP A3002 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM B3001 " 0.044 2.00e-02 2.50e+03 2.54e-02 1.46e+01 pdb=" C2C HEM B3001 " 0.023 2.00e-02 2.50e+03 pdb=" C3C HEM B3001 " 0.013 2.00e-02 2.50e+03 pdb=" C4C HEM B3001 " 0.003 2.00e-02 2.50e+03 pdb=" CAC HEM B3001 " -0.027 2.00e-02 2.50e+03 pdb=" CHC HEM B3001 " -0.049 2.00e-02 2.50e+03 pdb=" CHD HEM B3001 " -0.008 2.00e-02 2.50e+03 pdb=" CMC HEM B3001 " -0.001 2.00e-02 2.50e+03 pdb=" NC HEM B3001 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP D3002 " 0.054 2.00e-02 2.50e+03 3.41e-02 1.45e+01 pdb=" C3N NDP D3002 " 0.012 2.00e-02 2.50e+03 pdb=" C4N NDP D3002 " 0.007 2.00e-02 2.50e+03 pdb=" C7N NDP D3002 " -0.030 2.00e-02 2.50e+03 pdb=" N1N NDP D3002 " -0.043 2.00e-02 2.50e+03 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 5036 2.87 - 3.38: 15764 3.38 - 3.89: 30616 3.89 - 4.39: 35341 4.39 - 4.90: 58001 Nonbonded interactions: 144758 Sorted by model distance: nonbonded pdb=" OD1 ASP D 298 " pdb=" OG1 THR D 300 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASP C 298 " pdb=" OG1 THR C 300 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASP B 298 " pdb=" OG1 THR B 300 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASP A 298 " pdb=" OG1 THR A 300 " model vdw 2.369 3.040 nonbonded pdb=" O ARG A 388 " pdb=" O ASP A 389 " model vdw 2.369 3.040 ... (remaining 144753 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: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } 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: 1.380 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.110 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.014 0.212 16892 Z= 0.949 Angle : 1.675 23.631 23040 Z= 1.177 Chirality : 0.076 0.226 2328 Planarity : 0.005 0.035 3052 Dihedral : 14.337 94.395 6148 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.04 % Favored : 95.76 % Rotamer: Outliers : 0.99 % Allowed : 4.38 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -1.14 (0.17), residues: 1980 helix: -0.22 (0.17), residues: 680 sheet: -0.64 (0.29), residues: 276 loop : -1.11 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG B 72 TYR 0.025 0.004 TYR D 236 PHE 0.031 0.004 PHE D 334 TRP 0.017 0.004 TRP A 15 HIS 0.014 0.003 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.01399 (16888) covalent geometry : angle 1.67513 (23040) hydrogen bonds : bond 0.18097 ( 656) hydrogen bonds : angle 8.51332 ( 1872) Misc. bond : bond 0.01034 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 313 time to evaluate : 0.606 Fit side-chains REVERT: B 106 LYS cc_start: 0.7418 (mttt) cc_final: 0.7085 (mtmt) REVERT: B 201 SER cc_start: 0.7911 (t) cc_final: 0.7677 (p) REVERT: B 249 ASP cc_start: 0.6827 (m-30) cc_final: 0.6553 (t0) REVERT: B 255 GLN cc_start: 0.7417 (pt0) cc_final: 0.7117 (pp30) REVERT: B 392 MET cc_start: 0.8519 (mmm) cc_final: 0.7934 (mmm) REVERT: B 394 MET cc_start: 0.6569 (mpp) cc_final: 0.5721 (mpp) REVERT: B 428 GLU cc_start: 0.6028 (mp0) cc_final: 0.5637 (mp0) REVERT: B 457 LYS cc_start: 0.7312 (ttpt) cc_final: 0.6825 (ttmm) REVERT: B 476 LYS cc_start: 0.7055 (mttp) cc_final: 0.6851 (mptp) REVERT: B 488 ASP cc_start: 0.6799 (m-30) cc_final: 0.6400 (m-30) REVERT: B 492 HIS cc_start: 0.7138 (t-170) cc_final: 0.6854 (t-90) REVERT: B 499 LYS cc_start: 0.7043 (tttp) cc_final: 0.6351 (ttpp) REVERT: A 106 LYS cc_start: 0.7400 (mttt) cc_final: 0.7081 (mtmt) REVERT: A 201 SER cc_start: 0.7911 (t) cc_final: 0.7666 (p) REVERT: A 249 ASP cc_start: 0.6832 (m-30) cc_final: 0.6555 (t0) REVERT: A 255 GLN cc_start: 0.7409 (pt0) cc_final: 0.7119 (pp30) REVERT: A 392 MET cc_start: 0.8524 (mmm) cc_final: 0.8113 (mmm) REVERT: A 394 MET cc_start: 0.6546 (mpp) cc_final: 0.5724 (mpp) REVERT: A 428 GLU cc_start: 0.6063 (mp0) cc_final: 0.5676 (mp0) REVERT: A 457 LYS cc_start: 0.7133 (ttpt) cc_final: 0.6706 (ttmm) REVERT: A 476 LYS cc_start: 0.7000 (mttp) cc_final: 0.6791 (mptp) REVERT: A 492 HIS cc_start: 0.7173 (t-170) cc_final: 0.6951 (t-90) REVERT: A 499 LYS cc_start: 0.7029 (tttp) cc_final: 0.6343 (ttpp) REVERT: C 106 LYS cc_start: 0.7398 (mttt) cc_final: 0.7079 (mtmt) REVERT: C 201 SER cc_start: 0.7918 (t) cc_final: 0.7669 (p) REVERT: C 249 ASP cc_start: 0.6807 (m-30) cc_final: 0.6536 (t0) REVERT: C 255 GLN cc_start: 0.7407 (pt0) cc_final: 0.7173 (pp30) REVERT: C 392 MET cc_start: 0.8514 (mmm) cc_final: 0.8103 (mmm) REVERT: C 394 MET cc_start: 0.6454 (mpp) cc_final: 0.5673 (mpp) REVERT: C 428 GLU cc_start: 0.6082 (mp0) cc_final: 0.5711 (mp0) REVERT: C 457 LYS cc_start: 0.7138 (ttpt) cc_final: 0.6681 (ttmm) REVERT: C 471 GLN cc_start: 0.7281 (mt0) cc_final: 0.7031 (mt0) REVERT: C 476 LYS cc_start: 0.6905 (mttp) cc_final: 0.6699 (mptp) REVERT: C 488 ASP cc_start: 0.6795 (m-30) cc_final: 0.6385 (m-30) REVERT: C 492 HIS cc_start: 0.7136 (t-170) cc_final: 0.6842 (t-90) REVERT: C 499 LYS cc_start: 0.7039 (tttp) cc_final: 0.6352 (ttpp) REVERT: D 106 LYS cc_start: 0.7363 (mttt) cc_final: 0.7028 (mtmt) REVERT: D 201 SER cc_start: 0.7915 (t) cc_final: 0.7679 (p) REVERT: D 249 ASP cc_start: 0.6802 (m-30) cc_final: 0.6536 (t0) REVERT: D 255 GLN cc_start: 0.7407 (pt0) cc_final: 0.7147 (pp30) REVERT: D 392 MET cc_start: 0.8510 (mmm) cc_final: 0.7908 (mmm) REVERT: D 394 MET cc_start: 0.6578 (mpp) cc_final: 0.5721 (mpp) REVERT: D 428 GLU cc_start: 0.6063 (mp0) cc_final: 0.5691 (mp0) REVERT: D 457 LYS cc_start: 0.7340 (ttpt) cc_final: 0.6866 (ttmm) REVERT: D 471 GLN cc_start: 0.7287 (mt0) cc_final: 0.7042 (mt0) REVERT: D 488 ASP cc_start: 0.6797 (m-30) cc_final: 0.6389 (m-30) REVERT: D 492 HIS cc_start: 0.7194 (t-170) cc_final: 0.6914 (t-90) REVERT: D 499 LYS cc_start: 0.7105 (tttp) cc_final: 0.6406 (ttpp) outliers start: 17 outliers final: 4 residues processed: 321 average time/residue: 0.8053 time to fit residues: 280.3327 Evaluate side-chains 183 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 226 ASN B 338 ASN B 407 ASN A 22 GLN A 102 HIS A 226 ASN A 338 ASN A 407 ASN C 22 GLN C 102 HIS C 226 ASN C 338 ASN C 407 ASN D 22 GLN D 226 ASN D 338 ASN D 407 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.113027 restraints weight = 18872.435| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.27 r_work: 0.3144 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16892 Z= 0.118 Angle : 0.562 5.813 23040 Z= 0.288 Chirality : 0.044 0.150 2328 Planarity : 0.004 0.035 3052 Dihedral : 8.489 108.349 2260 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.87 % Allowed : 10.40 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.38 (0.19), residues: 1980 helix: 1.10 (0.20), residues: 688 sheet: 0.35 (0.30), residues: 300 loop : -0.31 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 430 TYR 0.016 0.001 TYR C 236 PHE 0.013 0.002 PHE C 57 TRP 0.008 0.001 TRP A 303 HIS 0.005 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00287 (16888) covalent geometry : angle 0.56185 (23040) hydrogen bonds : bond 0.04429 ( 656) hydrogen bonds : angle 5.87053 ( 1872) Misc. bond : bond 0.01951 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.652 Fit side-chains REVERT: B 19 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.6749 (ttm-80) REVERT: B 86 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: B 106 LYS cc_start: 0.7983 (mttt) cc_final: 0.7770 (mtmt) REVERT: B 389 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6352 (m-30) REVERT: B 499 LYS cc_start: 0.7685 (tttp) cc_final: 0.7157 (ttpp) REVERT: A 19 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.6723 (ttm-80) REVERT: A 389 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6457 (m-30) REVERT: A 499 LYS cc_start: 0.7664 (tttp) cc_final: 0.7129 (ttpp) REVERT: C 19 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.6745 (ttm-80) REVERT: C 389 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6459 (m-30) REVERT: C 476 LYS cc_start: 0.8106 (mttp) cc_final: 0.7894 (mtpp) REVERT: C 499 LYS cc_start: 0.7585 (tttp) cc_final: 0.7123 (ttpp) REVERT: D 19 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.6749 (ttm-80) REVERT: D 86 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: D 106 LYS cc_start: 0.8018 (mttt) cc_final: 0.7812 (mtmt) REVERT: D 377 CYS cc_start: 0.8217 (m) cc_final: 0.8006 (t) REVERT: D 389 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6356 (m-30) REVERT: D 499 LYS cc_start: 0.7632 (tttp) cc_final: 0.7142 (ttpp) outliers start: 32 outliers final: 8 residues processed: 227 average time/residue: 0.6695 time to fit residues: 167.2819 Evaluate side-chains 163 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS B 226 ASN B 338 ASN A 63 HIS A 102 HIS A 226 ASN A 338 ASN C 63 HIS C 102 HIS C 226 ASN C 338 ASN D 63 HIS D 226 ASN D 338 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107908 restraints weight = 19513.619| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.29 r_work: 0.3071 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16892 Z= 0.166 Angle : 0.600 6.698 23040 Z= 0.304 Chirality : 0.046 0.141 2328 Planarity : 0.004 0.041 3052 Dihedral : 8.901 120.810 2260 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.03 % Favored : 96.77 % Rotamer: Outliers : 2.63 % Allowed : 10.75 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.42 (0.19), residues: 1980 helix: 1.06 (0.20), residues: 684 sheet: 0.49 (0.32), residues: 272 loop : -0.25 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 363 TYR 0.019 0.002 TYR B 236 PHE 0.015 0.002 PHE A 136 TRP 0.012 0.002 TRP C 183 HIS 0.005 0.001 HIS D 372 Details of bonding type rmsd covalent geometry : bond 0.00421 (16888) covalent geometry : angle 0.60026 (23040) hydrogen bonds : bond 0.04934 ( 656) hydrogen bonds : angle 5.92027 ( 1872) Misc. bond : bond 0.01789 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.705 Fit side-chains REVERT: B 12 MET cc_start: 0.8581 (mtm) cc_final: 0.8203 (mtm) REVERT: B 19 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.6865 (ttm-80) REVERT: B 101 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: B 107 THR cc_start: 0.8180 (m) cc_final: 0.7804 (t) REVERT: B 424 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: B 437 ASP cc_start: 0.7333 (m-30) cc_final: 0.6767 (m-30) REVERT: B 499 LYS cc_start: 0.7696 (tttp) cc_final: 0.7152 (ttpp) REVERT: A 12 MET cc_start: 0.8590 (mtm) cc_final: 0.8214 (mtm) REVERT: A 19 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6865 (ttm-80) REVERT: A 101 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7477 (tp30) REVERT: A 107 THR cc_start: 0.8186 (m) cc_final: 0.7774 (t) REVERT: A 424 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: A 437 ASP cc_start: 0.7295 (m-30) cc_final: 0.6682 (m-30) REVERT: A 499 LYS cc_start: 0.7741 (tttp) cc_final: 0.7177 (ttpp) REVERT: C 12 MET cc_start: 0.8606 (mtm) cc_final: 0.8223 (mtm) REVERT: C 19 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.6863 (ttm-80) REVERT: C 101 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7469 (tp30) REVERT: C 107 THR cc_start: 0.8162 (m) cc_final: 0.7767 (t) REVERT: C 424 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: C 437 ASP cc_start: 0.7271 (m-30) cc_final: 0.6630 (m-30) REVERT: C 499 LYS cc_start: 0.7679 (tttp) cc_final: 0.7135 (ttpp) REVERT: D 12 MET cc_start: 0.8605 (mtm) cc_final: 0.8224 (mtm) REVERT: D 19 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6871 (ttm-80) REVERT: D 101 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7509 (tp30) REVERT: D 107 THR cc_start: 0.8179 (m) cc_final: 0.7814 (t) REVERT: D 424 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: D 437 ASP cc_start: 0.7275 (m-30) cc_final: 0.6670 (m-30) REVERT: D 499 LYS cc_start: 0.7694 (tttp) cc_final: 0.7155 (ttpp) outliers start: 45 outliers final: 16 residues processed: 200 average time/residue: 0.6697 time to fit residues: 147.5458 Evaluate side-chains 174 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS B 211 HIS B 226 ASN B 338 ASN A 14 HIS A 102 HIS A 211 HIS A 226 ASN A 338 ASN C 102 HIS C 211 HIS C 226 ASN C 338 ASN C 369 ASN D 14 HIS D 226 ASN D 338 ASN D 369 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.109428 restraints weight = 19308.677| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.31 r_work: 0.3097 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16892 Z= 0.125 Angle : 0.547 6.520 23040 Z= 0.275 Chirality : 0.044 0.137 2328 Planarity : 0.004 0.043 3052 Dihedral : 8.483 117.353 2260 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.87 % Allowed : 11.80 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.55 (0.19), residues: 1980 helix: 1.13 (0.20), residues: 684 sheet: 0.59 (0.33), residues: 276 loop : -0.15 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 363 TYR 0.017 0.001 TYR A 236 PHE 0.012 0.002 PHE A 136 TRP 0.010 0.001 TRP C 183 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00314 (16888) covalent geometry : angle 0.54720 (23040) hydrogen bonds : bond 0.04197 ( 656) hydrogen bonds : angle 5.68873 ( 1872) Misc. bond : bond 0.01332 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.566 Fit side-chains REVERT: B 101 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: B 107 THR cc_start: 0.8149 (m) cc_final: 0.7783 (t) REVERT: B 424 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: B 437 ASP cc_start: 0.7382 (m-30) cc_final: 0.6753 (m-30) REVERT: B 499 LYS cc_start: 0.7647 (tttp) cc_final: 0.7160 (ttpp) REVERT: A 23 LYS cc_start: 0.7441 (pttm) cc_final: 0.7203 (ptmt) REVERT: A 107 THR cc_start: 0.8149 (m) cc_final: 0.7787 (t) REVERT: A 424 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6702 (tm-30) REVERT: A 437 ASP cc_start: 0.7369 (m-30) cc_final: 0.6746 (m-30) REVERT: A 499 LYS cc_start: 0.7637 (tttp) cc_final: 0.7164 (ttpp) REVERT: C 23 LYS cc_start: 0.7433 (pttm) cc_final: 0.7211 (ptmt) REVERT: C 107 THR cc_start: 0.8147 (m) cc_final: 0.7783 (t) REVERT: C 437 ASP cc_start: 0.7339 (m-30) cc_final: 0.6712 (m-30) REVERT: C 499 LYS cc_start: 0.7717 (tttp) cc_final: 0.7205 (ttpp) REVERT: D 107 THR cc_start: 0.8151 (m) cc_final: 0.7784 (t) REVERT: D 424 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6682 (tm-30) REVERT: D 437 ASP cc_start: 0.7384 (m-30) cc_final: 0.6754 (m-30) REVERT: D 499 LYS cc_start: 0.7721 (tttp) cc_final: 0.7220 (ttpp) outliers start: 32 outliers final: 16 residues processed: 196 average time/residue: 0.6560 time to fit residues: 142.0476 Evaluate side-chains 182 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 149 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 338 ASN B 369 ASN A 226 ASN A 338 ASN A 369 ASN C 102 HIS C 226 ASN C 338 ASN D 211 HIS D 226 ASN D 338 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109461 restraints weight = 19163.284| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.31 r_work: 0.3101 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16892 Z= 0.126 Angle : 0.544 6.576 23040 Z= 0.273 Chirality : 0.044 0.137 2328 Planarity : 0.004 0.044 3052 Dihedral : 8.472 117.112 2260 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.81 % Allowed : 12.32 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.57 (0.19), residues: 1980 helix: 1.18 (0.20), residues: 684 sheet: 0.67 (0.33), residues: 276 loop : -0.18 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.017 0.001 TYR A 236 PHE 0.013 0.001 PHE D 136 TRP 0.012 0.001 TRP C 183 HIS 0.003 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00315 (16888) covalent geometry : angle 0.54423 (23040) hydrogen bonds : bond 0.04188 ( 656) hydrogen bonds : angle 5.64658 ( 1872) Misc. bond : bond 0.01270 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.584 Fit side-chains REVERT: B 101 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7208 (tp30) REVERT: B 107 THR cc_start: 0.8175 (m) cc_final: 0.7810 (t) REVERT: B 424 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6652 (tm-30) REVERT: B 437 ASP cc_start: 0.7396 (m-30) cc_final: 0.6994 (m-30) REVERT: B 499 LYS cc_start: 0.7685 (tttp) cc_final: 0.7135 (ttpp) REVERT: A 101 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7248 (tp30) REVERT: A 107 THR cc_start: 0.8173 (m) cc_final: 0.7809 (t) REVERT: A 424 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.6689 (tm-30) REVERT: A 437 ASP cc_start: 0.7376 (m-30) cc_final: 0.6966 (m-30) REVERT: A 499 LYS cc_start: 0.7690 (tttp) cc_final: 0.7145 (ttpp) REVERT: C 101 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7294 (tp30) REVERT: C 107 THR cc_start: 0.8160 (m) cc_final: 0.7796 (t) REVERT: C 424 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: C 437 ASP cc_start: 0.7353 (m-30) cc_final: 0.6676 (m-30) REVERT: C 499 LYS cc_start: 0.7707 (tttp) cc_final: 0.7144 (ttpp) REVERT: D 101 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: D 107 THR cc_start: 0.8172 (m) cc_final: 0.7810 (t) REVERT: D 424 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6669 (tm-30) REVERT: D 437 ASP cc_start: 0.7385 (m-30) cc_final: 0.6976 (m-30) REVERT: D 499 LYS cc_start: 0.7697 (tttp) cc_final: 0.7160 (ttpp) outliers start: 31 outliers final: 19 residues processed: 196 average time/residue: 0.6536 time to fit residues: 141.4842 Evaluate side-chains 192 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 188 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 338 ASN B 439 ASN A 226 ASN A 338 ASN A 439 ASN C 226 ASN C 338 ASN D 226 ASN D 338 ASN D 439 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109884 restraints weight = 19265.027| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.30 r_work: 0.3106 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16892 Z= 0.121 Angle : 0.538 6.510 23040 Z= 0.269 Chirality : 0.044 0.138 2328 Planarity : 0.004 0.044 3052 Dihedral : 8.358 117.344 2260 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.93 % Allowed : 12.21 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.60 (0.19), residues: 1980 helix: 1.24 (0.20), residues: 684 sheet: 0.63 (0.33), residues: 276 loop : -0.18 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.017 0.001 TYR C 236 PHE 0.013 0.001 PHE B 136 TRP 0.011 0.001 TRP A 183 HIS 0.003 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00304 (16888) covalent geometry : angle 0.53751 (23040) hydrogen bonds : bond 0.04058 ( 656) hydrogen bonds : angle 5.60700 ( 1872) Misc. bond : bond 0.01456 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.640 Fit side-chains REVERT: B 107 THR cc_start: 0.8184 (m) cc_final: 0.7821 (t) REVERT: B 249 ASP cc_start: 0.7759 (m-30) cc_final: 0.7480 (t0) REVERT: B 424 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: B 437 ASP cc_start: 0.7426 (m-30) cc_final: 0.6755 (m-30) REVERT: B 458 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.7884 (mtm180) REVERT: B 499 LYS cc_start: 0.7688 (tttp) cc_final: 0.7151 (ttpp) REVERT: A 101 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7284 (tp30) REVERT: A 107 THR cc_start: 0.8204 (m) cc_final: 0.7853 (t) REVERT: A 249 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7493 (t0) REVERT: A 424 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: A 437 ASP cc_start: 0.7401 (m-30) cc_final: 0.6707 (m-30) REVERT: A 458 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.7892 (mtm180) REVERT: A 499 LYS cc_start: 0.7690 (tttp) cc_final: 0.7158 (ttpp) REVERT: C 101 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7308 (tp30) REVERT: C 107 THR cc_start: 0.8187 (m) cc_final: 0.7837 (t) REVERT: C 249 ASP cc_start: 0.7762 (m-30) cc_final: 0.7490 (t0) REVERT: C 424 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: C 437 ASP cc_start: 0.7359 (m-30) cc_final: 0.6945 (m-30) REVERT: C 458 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.7913 (mtm180) REVERT: C 499 LYS cc_start: 0.7701 (tttp) cc_final: 0.7169 (ttpp) REVERT: D 101 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7312 (tp30) REVERT: D 107 THR cc_start: 0.8186 (m) cc_final: 0.7821 (t) REVERT: D 249 ASP cc_start: 0.7788 (m-30) cc_final: 0.7501 (t0) REVERT: D 424 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6688 (tm-30) REVERT: D 437 ASP cc_start: 0.7399 (m-30) cc_final: 0.6721 (m-30) REVERT: D 458 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.7906 (mtm180) REVERT: D 499 LYS cc_start: 0.7703 (tttp) cc_final: 0.7161 (ttpp) outliers start: 33 outliers final: 20 residues processed: 197 average time/residue: 0.6278 time to fit residues: 137.0556 Evaluate side-chains 190 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS B 226 ASN B 338 ASN A 226 ASN A 338 ASN C 226 ASN C 338 ASN C 439 ASN D 102 HIS D 226 ASN D 338 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.111219 restraints weight = 19196.242| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.29 r_work: 0.3127 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16892 Z= 0.105 Angle : 0.517 6.423 23040 Z= 0.258 Chirality : 0.043 0.137 2328 Planarity : 0.004 0.043 3052 Dihedral : 7.953 111.264 2260 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.28 % Allowed : 11.80 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.70 (0.19), residues: 1980 helix: 1.39 (0.20), residues: 680 sheet: 0.66 (0.33), residues: 276 loop : -0.16 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 382 TYR 0.016 0.001 TYR D 84 PHE 0.012 0.001 PHE A 136 TRP 0.010 0.001 TRP C 183 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00259 (16888) covalent geometry : angle 0.51716 (23040) hydrogen bonds : bond 0.03712 ( 656) hydrogen bonds : angle 5.48286 ( 1872) Misc. bond : bond 0.01363 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.682 Fit side-chains REVERT: B 59 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7972 (t0) REVERT: B 107 THR cc_start: 0.8162 (m) cc_final: 0.7799 (t) REVERT: B 249 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7466 (t0) REVERT: B 424 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6721 (tm-30) REVERT: B 437 ASP cc_start: 0.7354 (m-30) cc_final: 0.6832 (m-30) REVERT: B 458 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.7878 (mtm180) REVERT: B 499 LYS cc_start: 0.7671 (tttp) cc_final: 0.7129 (ttpp) REVERT: A 107 THR cc_start: 0.8147 (m) cc_final: 0.7797 (t) REVERT: A 249 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7461 (t0) REVERT: A 424 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: A 437 ASP cc_start: 0.7324 (m-30) cc_final: 0.6778 (m-30) REVERT: A 458 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.7868 (mtm180) REVERT: A 499 LYS cc_start: 0.7676 (tttp) cc_final: 0.7135 (ttpp) REVERT: C 107 THR cc_start: 0.8139 (m) cc_final: 0.7783 (t) REVERT: C 249 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7463 (t0) REVERT: C 424 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: C 437 ASP cc_start: 0.7363 (m-30) cc_final: 0.6825 (m-30) REVERT: C 458 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.7906 (mtm180) REVERT: C 499 LYS cc_start: 0.7683 (tttp) cc_final: 0.7157 (ttpp) REVERT: D 107 THR cc_start: 0.8170 (m) cc_final: 0.7812 (t) REVERT: D 249 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7435 (t0) REVERT: D 424 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: D 437 ASP cc_start: 0.7351 (m-30) cc_final: 0.7042 (m-30) REVERT: D 458 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.7900 (mtm180) REVERT: D 499 LYS cc_start: 0.7680 (tttp) cc_final: 0.7144 (ttpp) outliers start: 39 outliers final: 16 residues processed: 208 average time/residue: 0.6324 time to fit residues: 146.0428 Evaluate side-chains 193 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 145 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS B 226 ASN B 338 ASN A 102 HIS A 226 ASN A 338 ASN C 102 HIS C 226 ASN C 338 ASN D 102 HIS D 226 ASN D 338 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.109782 restraints weight = 19241.371| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.30 r_work: 0.3107 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16892 Z= 0.127 Angle : 0.542 6.526 23040 Z= 0.271 Chirality : 0.044 0.140 2328 Planarity : 0.004 0.044 3052 Dihedral : 8.255 112.934 2260 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.99 % Allowed : 11.80 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.65 (0.19), residues: 1980 helix: 1.29 (0.20), residues: 684 sheet: 0.56 (0.33), residues: 276 loop : -0.12 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 363 TYR 0.017 0.001 TYR C 236 PHE 0.013 0.001 PHE C 136 TRP 0.012 0.001 TRP C 183 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00321 (16888) covalent geometry : angle 0.54199 (23040) hydrogen bonds : bond 0.04099 ( 656) hydrogen bonds : angle 5.61948 ( 1872) Misc. bond : bond 0.01463 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.736 Fit side-chains REVERT: B 59 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8082 (t0) REVERT: B 107 THR cc_start: 0.8169 (m) cc_final: 0.7824 (t) REVERT: B 249 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7446 (t0) REVERT: B 424 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: B 437 ASP cc_start: 0.7402 (m-30) cc_final: 0.7099 (m-30) REVERT: B 458 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7898 (mtm180) REVERT: B 499 LYS cc_start: 0.7646 (tttp) cc_final: 0.7162 (ttpp) REVERT: A 12 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8193 (mtm) REVERT: A 101 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: A 107 THR cc_start: 0.8199 (m) cc_final: 0.7852 (t) REVERT: A 249 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7435 (t0) REVERT: A 424 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: A 437 ASP cc_start: 0.7380 (m-30) cc_final: 0.6841 (m-30) REVERT: A 458 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7914 (mtm180) REVERT: A 499 LYS cc_start: 0.7642 (tttp) cc_final: 0.7167 (ttpp) REVERT: C 101 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7289 (tp30) REVERT: C 107 THR cc_start: 0.8189 (m) cc_final: 0.7841 (t) REVERT: C 249 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7436 (t0) REVERT: C 424 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: C 437 ASP cc_start: 0.7393 (m-30) cc_final: 0.6851 (m-30) REVERT: C 458 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.7919 (mtm180) REVERT: C 499 LYS cc_start: 0.7619 (tttp) cc_final: 0.7168 (ttpp) REVERT: D 59 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8084 (t0) REVERT: D 101 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: D 107 THR cc_start: 0.8165 (m) cc_final: 0.7815 (t) REVERT: D 249 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7446 (t0) REVERT: D 424 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: D 437 ASP cc_start: 0.7397 (m-30) cc_final: 0.6873 (m-30) REVERT: D 458 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.7912 (mtm180) REVERT: D 499 LYS cc_start: 0.7652 (tttp) cc_final: 0.7169 (ttpp) outliers start: 34 outliers final: 15 residues processed: 193 average time/residue: 0.6365 time to fit residues: 136.1437 Evaluate side-chains 201 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 181 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 338 ASN A 226 ASN A 338 ASN C 226 ASN C 338 ASN D 226 ASN D 338 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109139 restraints weight = 19203.460| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.26 r_work: 0.3098 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16892 Z= 0.145 Angle : 0.561 6.654 23040 Z= 0.282 Chirality : 0.045 0.143 2328 Planarity : 0.004 0.046 3052 Dihedral : 8.404 116.827 2260 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.34 % Allowed : 11.39 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.63 (0.19), residues: 1980 helix: 1.18 (0.20), residues: 684 sheet: 0.32 (0.32), residues: 304 loop : 0.01 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 363 TYR 0.018 0.002 TYR D 236 PHE 0.014 0.002 PHE C 136 TRP 0.012 0.001 TRP B 183 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00365 (16888) covalent geometry : angle 0.56087 (23040) hydrogen bonds : bond 0.04354 ( 656) hydrogen bonds : angle 5.72668 ( 1872) Misc. bond : bond 0.01618 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.688 Fit side-chains REVERT: B 59 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8143 (t0) REVERT: B 107 THR cc_start: 0.8187 (m) cc_final: 0.7838 (t) REVERT: B 249 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7435 (t0) REVERT: B 424 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.6794 (tm-30) REVERT: B 437 ASP cc_start: 0.7423 (m-30) cc_final: 0.6901 (m-30) REVERT: B 458 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.7876 (mtm180) REVERT: B 488 ASP cc_start: 0.7582 (m-30) cc_final: 0.7351 (m-30) REVERT: B 499 LYS cc_start: 0.7655 (tttp) cc_final: 0.7168 (ttpp) REVERT: A 12 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8179 (mtm) REVERT: A 101 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: A 107 THR cc_start: 0.8178 (m) cc_final: 0.7835 (t) REVERT: A 249 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7440 (t0) REVERT: A 424 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6788 (tm-30) REVERT: A 437 ASP cc_start: 0.7399 (m-30) cc_final: 0.6863 (m-30) REVERT: A 458 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7887 (mtm180) REVERT: A 488 ASP cc_start: 0.7622 (m-30) cc_final: 0.7318 (m-30) REVERT: A 499 LYS cc_start: 0.7704 (tttp) cc_final: 0.7204 (ttpp) REVERT: C 101 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: C 107 THR cc_start: 0.8164 (m) cc_final: 0.7819 (t) REVERT: C 249 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7447 (t0) REVERT: C 424 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: C 437 ASP cc_start: 0.7404 (m-30) cc_final: 0.6887 (m-30) REVERT: C 458 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7893 (mtm180) REVERT: C 488 ASP cc_start: 0.7523 (m-30) cc_final: 0.7288 (m-30) REVERT: C 499 LYS cc_start: 0.7641 (tttp) cc_final: 0.7175 (ttpp) REVERT: D 12 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8150 (mtm) REVERT: D 59 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8152 (t0) REVERT: D 101 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: D 107 THR cc_start: 0.8173 (m) cc_final: 0.7830 (t) REVERT: D 249 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7448 (t0) REVERT: D 424 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: D 437 ASP cc_start: 0.7410 (m-30) cc_final: 0.6886 (m-30) REVERT: D 458 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7905 (mtm180) REVERT: D 488 ASP cc_start: 0.7527 (m-30) cc_final: 0.7286 (m-30) REVERT: D 499 LYS cc_start: 0.7659 (tttp) cc_final: 0.7173 (ttpp) outliers start: 40 outliers final: 15 residues processed: 198 average time/residue: 0.6904 time to fit residues: 150.4217 Evaluate side-chains 193 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 72 optimal weight: 7.9990 chunk 172 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 51 optimal weight: 0.0050 chunk 128 optimal weight: 0.0980 chunk 149 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 141 optimal weight: 0.0060 chunk 183 optimal weight: 2.9990 chunk 3 optimal weight: 0.0470 chunk 124 optimal weight: 7.9990 overall best weight: 0.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 338 ASN B 387 GLN A 102 HIS A 226 ASN A 338 ASN A 387 GLN C 102 HIS C 226 ASN C 338 ASN C 387 GLN D 226 ASN D 338 ASN D 387 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.115888 restraints weight = 19212.735| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.25 r_work: 0.3196 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16892 Z= 0.086 Angle : 0.497 6.222 23040 Z= 0.246 Chirality : 0.042 0.138 2328 Planarity : 0.004 0.043 3052 Dihedral : 7.118 93.175 2260 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.34 % Allowed : 12.73 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.86 (0.19), residues: 1980 helix: 1.48 (0.20), residues: 676 sheet: 0.51 (0.32), residues: 304 loop : 0.05 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 382 TYR 0.013 0.001 TYR D 236 PHE 0.010 0.001 PHE C 473 TRP 0.011 0.001 TRP A 183 HIS 0.005 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00198 (16888) covalent geometry : angle 0.49717 (23040) hydrogen bonds : bond 0.03097 ( 656) hydrogen bonds : angle 5.29306 ( 1872) Misc. bond : bond 0.00175 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.609 Fit side-chains REVERT: B 25 ASP cc_start: 0.7640 (m-30) cc_final: 0.7426 (t0) REVERT: B 107 THR cc_start: 0.8038 (m) cc_final: 0.7700 (t) REVERT: B 249 ASP cc_start: 0.7693 (m-30) cc_final: 0.7434 (t0) REVERT: B 437 ASP cc_start: 0.7302 (m-30) cc_final: 0.6763 (m-30) REVERT: B 458 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7813 (mtm180) REVERT: B 499 LYS cc_start: 0.7614 (tttp) cc_final: 0.7102 (ttpp) REVERT: A 25 ASP cc_start: 0.7682 (m-30) cc_final: 0.7464 (t0) REVERT: A 107 THR cc_start: 0.8051 (m) cc_final: 0.7720 (t) REVERT: A 249 ASP cc_start: 0.7683 (m-30) cc_final: 0.7436 (t0) REVERT: A 437 ASP cc_start: 0.7294 (m-30) cc_final: 0.6733 (m-30) REVERT: A 458 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7867 (mtm180) REVERT: A 499 LYS cc_start: 0.7646 (tttp) cc_final: 0.7127 (ttpp) REVERT: C 25 ASP cc_start: 0.7661 (m-30) cc_final: 0.7444 (t0) REVERT: C 107 THR cc_start: 0.8033 (m) cc_final: 0.7699 (t) REVERT: C 249 ASP cc_start: 0.7693 (m-30) cc_final: 0.7438 (t0) REVERT: C 424 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: C 437 ASP cc_start: 0.7322 (m-30) cc_final: 0.6771 (m-30) REVERT: C 458 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7875 (mtm180) REVERT: C 499 LYS cc_start: 0.7639 (tttp) cc_final: 0.7123 (ttpp) REVERT: D 25 ASP cc_start: 0.7675 (m-30) cc_final: 0.7453 (t0) REVERT: D 107 THR cc_start: 0.8046 (m) cc_final: 0.7707 (t) REVERT: D 249 ASP cc_start: 0.7701 (m-30) cc_final: 0.7431 (t0) REVERT: D 437 ASP cc_start: 0.7308 (m-30) cc_final: 0.6747 (m-30) REVERT: D 458 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.7880 (mtm180) REVERT: D 499 LYS cc_start: 0.7646 (tttp) cc_final: 0.7122 (ttpp) outliers start: 23 outliers final: 18 residues processed: 217 average time/residue: 0.6241 time to fit residues: 150.0437 Evaluate side-chains 186 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 118 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 41 optimal weight: 0.0570 chunk 114 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 157 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS B 226 ASN B 338 ASN B 439 ASN A 226 ASN A 338 ASN A 439 ASN C 226 ASN C 338 ASN C 439 ASN D 102 HIS D 226 ASN D 338 ASN D 439 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.129118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109218 restraints weight = 19246.140| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.28 r_work: 0.3095 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16892 Z= 0.151 Angle : 0.568 6.711 23040 Z= 0.285 Chirality : 0.045 0.139 2328 Planarity : 0.004 0.047 3052 Dihedral : 8.007 97.321 2260 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.11 % Allowed : 14.60 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.73 (0.19), residues: 1980 helix: 1.28 (0.20), residues: 684 sheet: 0.44 (0.32), residues: 304 loop : 0.03 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 363 TYR 0.018 0.002 TYR C 236 PHE 0.015 0.002 PHE D 136 TRP 0.014 0.002 TRP D 183 HIS 0.005 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00381 (16888) covalent geometry : angle 0.56779 (23040) hydrogen bonds : bond 0.04425 ( 656) hydrogen bonds : angle 5.67602 ( 1872) Misc. bond : bond 0.02552 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5022.89 seconds wall clock time: 86 minutes 32.24 seconds (5192.24 seconds total)