Starting phenix.real_space_refine on Tue Dec 31 18:44:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wzj_37954/12_2024/8wzj_37954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wzj_37954/12_2024/8wzj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wzj_37954/12_2024/8wzj_37954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wzj_37954/12_2024/8wzj_37954.map" model { file = "/net/cci-nas-00/data/ceres_data/8wzj_37954/12_2024/8wzj_37954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wzj_37954/12_2024/8wzj_37954.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16368 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: "A" 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: C, B, D Time building chain proxies: 8.91, per 1000 atoms: 0.54 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: 3.80 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.85 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: 5.17 Time building geometry restraints manager: 4.45 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 0.790 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 35.830 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.590 ------------------------------------------------------------------------------- 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 16888 Z= 0.916 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (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 TRP 0.017 0.004 TRP A 15 HIS 0.014 0.003 HIS C 218 PHE 0.031 0.004 PHE D 334 TYR 0.025 0.004 TYR D 236 ARG 0.022 0.002 ARG B 72 *********************** 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 : 1.961 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: 1.7065 time to fit residues: 595.1830 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 : 1.942 ------------------------------------------------------------------------------- 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 165 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16888 Z= 0.219 Angle : 0.583 5.965 23040 Z= 0.299 Chirality : 0.045 0.147 2328 Planarity : 0.004 0.035 3052 Dihedral : 8.783 114.133 2260 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.52 % Allowed : 10.51 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.18), residues: 1980 helix: 1.03 (0.20), residues: 688 sheet: 0.32 (0.31), residues: 284 loop : -0.34 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 303 HIS 0.005 0.001 HIS A 102 PHE 0.013 0.002 PHE C 57 TYR 0.017 0.001 TYR C 236 ARG 0.003 0.001 ARG C 365 *********************** 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 216 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 1.911 Fit side-chains REVERT: B 12 MET cc_start: 0.7340 (mmm) cc_final: 0.7084 (mtm) REVERT: B 19 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5789 (ttm-80) REVERT: B 60 GLU cc_start: 0.6996 (tt0) cc_final: 0.6792 (tt0) REVERT: B 106 LYS cc_start: 0.7317 (mttt) cc_final: 0.6918 (mttp) REVERT: B 201 SER cc_start: 0.7950 (t) cc_final: 0.7606 (p) REVERT: B 389 ASP cc_start: 0.5667 (OUTLIER) cc_final: 0.5032 (m-30) REVERT: B 476 LYS cc_start: 0.6773 (mttp) cc_final: 0.6381 (mtpp) REVERT: B 499 LYS cc_start: 0.6988 (tttp) cc_final: 0.6306 (ttpp) REVERT: A 12 MET cc_start: 0.7310 (mmm) cc_final: 0.7073 (mtm) REVERT: A 19 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.5782 (ttm-80) REVERT: A 106 LYS cc_start: 0.7279 (mttt) cc_final: 0.6907 (mttp) REVERT: A 107 THR cc_start: 0.7260 (m) cc_final: 0.6622 (t) REVERT: A 201 SER cc_start: 0.7949 (t) cc_final: 0.7600 (p) REVERT: A 389 ASP cc_start: 0.5672 (OUTLIER) cc_final: 0.5147 (m-30) REVERT: A 476 LYS cc_start: 0.6781 (mttp) cc_final: 0.6399 (mtpp) REVERT: A 499 LYS cc_start: 0.6977 (tttp) cc_final: 0.6299 (ttpp) REVERT: C 12 MET cc_start: 0.7319 (mmm) cc_final: 0.7081 (mtm) REVERT: C 19 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.5778 (ttm-80) REVERT: C 106 LYS cc_start: 0.7279 (mttt) cc_final: 0.6910 (mttp) REVERT: C 107 THR cc_start: 0.7261 (m) cc_final: 0.6626 (t) REVERT: C 201 SER cc_start: 0.7917 (t) cc_final: 0.7635 (p) REVERT: C 389 ASP cc_start: 0.5668 (OUTLIER) cc_final: 0.5145 (m-30) REVERT: C 476 LYS cc_start: 0.6736 (mttp) cc_final: 0.6365 (mtpp) REVERT: C 499 LYS cc_start: 0.6951 (tttp) cc_final: 0.6291 (ttpp) REVERT: D 12 MET cc_start: 0.7345 (mmm) cc_final: 0.7094 (mtm) REVERT: D 19 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.5795 (ttm-80) REVERT: D 60 GLU cc_start: 0.6998 (tt0) cc_final: 0.6796 (tt0) REVERT: D 106 LYS cc_start: 0.7309 (mttt) cc_final: 0.6909 (mttp) REVERT: D 201 SER cc_start: 0.7988 (t) cc_final: 0.7651 (p) REVERT: D 255 GLN cc_start: 0.7303 (pt0) cc_final: 0.7093 (pp30) REVERT: D 389 ASP cc_start: 0.5668 (OUTLIER) cc_final: 0.5028 (m-30) REVERT: D 499 LYS cc_start: 0.6959 (tttp) cc_final: 0.6293 (ttpp) outliers start: 26 outliers final: 8 residues processed: 212 average time/residue: 1.4379 time to fit residues: 336.3282 Evaluate side-chains 176 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG 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 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 98 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16888 Z= 0.208 Angle : 0.555 6.517 23040 Z= 0.281 Chirality : 0.044 0.136 2328 Planarity : 0.004 0.038 3052 Dihedral : 8.429 114.894 2260 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.08 % Favored : 96.72 % Rotamer: Outliers : 2.69 % Allowed : 11.92 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 1980 helix: 1.18 (0.20), residues: 684 sheet: 0.57 (0.32), residues: 272 loop : -0.21 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.004 0.001 HIS C 102 PHE 0.013 0.002 PHE B 57 TYR 0.017 0.001 TYR D 236 ARG 0.004 0.000 ARG D 382 *********************** 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 234 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 1.950 Fit side-chains REVERT: B 19 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.5779 (ttm-80) REVERT: B 60 GLU cc_start: 0.6993 (tt0) cc_final: 0.6777 (tt0) REVERT: B 101 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7167 (tp30) REVERT: B 106 LYS cc_start: 0.7253 (mttt) cc_final: 0.6889 (mttp) REVERT: B 107 THR cc_start: 0.7238 (m) cc_final: 0.6615 (t) REVERT: B 249 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6445 (t0) REVERT: B 298 ASP cc_start: 0.7916 (t0) cc_final: 0.7573 (t70) REVERT: B 377 CYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7412 (t) REVERT: B 424 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.5889 (tm-30) REVERT: B 437 ASP cc_start: 0.6279 (m-30) cc_final: 0.5802 (m-30) REVERT: B 499 LYS cc_start: 0.6951 (tttp) cc_final: 0.6274 (ttpp) REVERT: A 19 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.5779 (ttm-80) REVERT: A 106 LYS cc_start: 0.7242 (mttt) cc_final: 0.6882 (mttp) REVERT: A 107 THR cc_start: 0.7271 (m) cc_final: 0.6651 (t) REVERT: A 249 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6402 (t0) REVERT: A 298 ASP cc_start: 0.7929 (t0) cc_final: 0.7587 (t70) REVERT: A 377 CYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7414 (t) REVERT: A 424 GLN cc_start: 0.6617 (OUTLIER) cc_final: 0.5911 (tm-30) REVERT: A 437 ASP cc_start: 0.6267 (m-30) cc_final: 0.5754 (m-30) REVERT: A 499 LYS cc_start: 0.6951 (tttp) cc_final: 0.6275 (ttpp) REVERT: C 19 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.5770 (ttm-80) REVERT: C 101 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7208 (tp30) REVERT: C 106 LYS cc_start: 0.7239 (mttt) cc_final: 0.6886 (mttp) REVERT: C 107 THR cc_start: 0.7269 (m) cc_final: 0.6651 (t) REVERT: C 249 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6426 (t0) REVERT: C 298 ASP cc_start: 0.7930 (t0) cc_final: 0.7594 (t70) REVERT: C 377 CYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7408 (t) REVERT: C 424 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6466 (tm-30) REVERT: C 437 ASP cc_start: 0.6270 (m-30) cc_final: 0.5754 (m-30) REVERT: C 499 LYS cc_start: 0.6942 (tttp) cc_final: 0.6268 (ttpp) REVERT: D 19 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5780 (ttm-80) REVERT: D 60 GLU cc_start: 0.6975 (tt0) cc_final: 0.6759 (tt0) REVERT: D 101 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7206 (tp30) REVERT: D 106 LYS cc_start: 0.7251 (mttt) cc_final: 0.6887 (mttp) REVERT: D 107 THR cc_start: 0.7248 (m) cc_final: 0.6627 (t) REVERT: D 201 SER cc_start: 0.7887 (t) cc_final: 0.7622 (p) REVERT: D 249 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6380 (t0) REVERT: D 298 ASP cc_start: 0.7895 (t0) cc_final: 0.7563 (t70) REVERT: D 424 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.5895 (tm-30) REVERT: D 437 ASP cc_start: 0.6274 (m-30) cc_final: 0.5755 (m-30) REVERT: D 499 LYS cc_start: 0.6950 (tttp) cc_final: 0.6274 (ttpp) outliers start: 46 outliers final: 16 residues processed: 219 average time/residue: 1.3637 time to fit residues: 331.0175 Evaluate side-chains 195 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 1.839 ------------------------------------------------------------------------------- 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 249 ASP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 377 CYS 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 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 377 CYS 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 249 ASP Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 377 CYS 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 119 optimal weight: 0.0770 chunk 178 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS B 226 ASN B 305 HIS B 338 ASN A 102 HIS A 226 ASN A 305 HIS A 338 ASN C 102 HIS C 226 ASN C 305 HIS C 338 ASN D 226 ASN D 338 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16888 Z= 0.205 Angle : 0.549 6.499 23040 Z= 0.276 Chirality : 0.044 0.137 2328 Planarity : 0.004 0.038 3052 Dihedral : 8.463 116.710 2260 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.92 % Allowed : 11.57 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1980 helix: 1.22 (0.20), residues: 684 sheet: 0.65 (0.33), residues: 276 loop : -0.16 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 183 HIS 0.003 0.001 HIS A 102 PHE 0.013 0.002 PHE C 136 TYR 0.017 0.001 TYR B 236 ARG 0.003 0.000 ARG D 382 *********************** 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 234 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 1.671 Fit side-chains REVERT: B 23 LYS cc_start: 0.6886 (pttm) cc_final: 0.6654 (ptmt) REVERT: B 60 GLU cc_start: 0.6952 (tt0) cc_final: 0.6716 (mt-10) REVERT: B 101 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6949 (tp30) REVERT: B 106 LYS cc_start: 0.7278 (mttt) cc_final: 0.6894 (mttp) REVERT: B 107 THR cc_start: 0.7262 (m) cc_final: 0.6658 (t) REVERT: B 201 SER cc_start: 0.7920 (OUTLIER) cc_final: 0.7609 (p) REVERT: B 298 ASP cc_start: 0.7954 (t0) cc_final: 0.7581 (t70) REVERT: B 377 CYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7362 (t) REVERT: B 424 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.5910 (tm-30) REVERT: B 437 ASP cc_start: 0.6508 (m-30) cc_final: 0.6009 (m-30) REVERT: B 499 LYS cc_start: 0.6937 (tttp) cc_final: 0.6305 (ttpp) REVERT: A 12 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6879 (mtp) REVERT: A 101 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6857 (tp30) REVERT: A 106 LYS cc_start: 0.7248 (mttt) cc_final: 0.6933 (mttp) REVERT: A 107 THR cc_start: 0.7266 (m) cc_final: 0.6662 (t) REVERT: A 119 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6798 (mp0) REVERT: A 201 SER cc_start: 0.7920 (OUTLIER) cc_final: 0.7609 (p) REVERT: A 249 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6499 (t0) REVERT: A 298 ASP cc_start: 0.7979 (t0) cc_final: 0.7601 (t70) REVERT: A 377 CYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7372 (t) REVERT: A 424 GLN cc_start: 0.6577 (OUTLIER) cc_final: 0.5864 (tm-30) REVERT: A 437 ASP cc_start: 0.6475 (m-30) cc_final: 0.5968 (m-30) REVERT: A 499 LYS cc_start: 0.6941 (tttp) cc_final: 0.6309 (ttpp) REVERT: C 101 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6947 (tp30) REVERT: C 106 LYS cc_start: 0.7248 (mttt) cc_final: 0.6935 (mttp) REVERT: C 107 THR cc_start: 0.7265 (m) cc_final: 0.6663 (t) REVERT: C 119 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6765 (mp0) REVERT: C 201 SER cc_start: 0.7924 (OUTLIER) cc_final: 0.7611 (p) REVERT: C 249 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6499 (t0) REVERT: C 298 ASP cc_start: 0.7986 (t0) cc_final: 0.7648 (t0) REVERT: C 377 CYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7388 (t) REVERT: C 424 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: C 437 ASP cc_start: 0.6466 (m-30) cc_final: 0.5948 (m-30) REVERT: C 499 LYS cc_start: 0.6944 (tttp) cc_final: 0.6300 (ttpp) REVERT: D 23 LYS cc_start: 0.6895 (pttm) cc_final: 0.6665 (ptmt) REVERT: D 60 GLU cc_start: 0.6994 (tt0) cc_final: 0.6766 (mt-10) REVERT: D 101 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6987 (tp30) REVERT: D 106 LYS cc_start: 0.7276 (mttt) cc_final: 0.6896 (mttp) REVERT: D 107 THR cc_start: 0.7267 (m) cc_final: 0.6663 (t) REVERT: D 298 ASP cc_start: 0.7982 (t0) cc_final: 0.7600 (t70) REVERT: D 424 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.5870 (tm-30) REVERT: D 437 ASP cc_start: 0.6482 (m-30) cc_final: 0.5973 (m-30) REVERT: D 499 LYS cc_start: 0.6947 (tttp) cc_final: 0.6248 (ttpp) outliers start: 50 outliers final: 20 residues processed: 223 average time/residue: 1.4567 time to fit residues: 359.5712 Evaluate side-chains 207 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 201 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 377 CYS 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 180 ASP Chi-restraints excluded: chain A residue 201 SER 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 377 CYS 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 201 SER 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 377 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 235 HIS B 338 ASN B 362 HIS B 369 ASN B 439 ASN A 14 HIS A 102 HIS A 226 ASN A 235 HIS A 338 ASN A 362 HIS A 369 ASN A 439 ASN C 14 HIS C 226 ASN C 235 HIS C 338 ASN C 369 ASN C 439 ASN D 14 HIS D 226 ASN D 235 HIS D 338 ASN D 362 HIS D 369 ASN D 439 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.104 16888 Z= 0.652 Angle : 0.812 10.270 23040 Z= 0.410 Chirality : 0.056 0.164 2328 Planarity : 0.007 0.045 3052 Dihedral : 10.174 141.405 2260 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.15 % Allowed : 12.44 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 1980 helix: 0.43 (0.19), residues: 684 sheet: 0.67 (0.33), residues: 272 loop : -0.62 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 15 HIS 0.009 0.002 HIS D 305 PHE 0.019 0.004 PHE C 136 TYR 0.022 0.003 TYR D 236 ARG 0.006 0.001 ARG B 72 *********************** 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 224 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 2.123 Fit side-chains REVERT: B 12 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.7030 (mtm) REVERT: B 106 LYS cc_start: 0.7142 (mttt) cc_final: 0.6831 (mttp) REVERT: B 107 THR cc_start: 0.7413 (m) cc_final: 0.6759 (t) REVERT: B 119 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: B 424 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.5982 (tm-30) REVERT: B 437 ASP cc_start: 0.6715 (m-30) cc_final: 0.6339 (m-30) REVERT: B 457 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7038 (ttmm) REVERT: B 499 LYS cc_start: 0.6883 (tttp) cc_final: 0.6296 (ttpp) REVERT: A 101 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7350 (tp30) REVERT: A 106 LYS cc_start: 0.7140 (mttt) cc_final: 0.6831 (mttp) REVERT: A 107 THR cc_start: 0.7418 (m) cc_final: 0.6753 (t) REVERT: A 249 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6771 (t0) REVERT: A 424 GLN cc_start: 0.6711 (OUTLIER) cc_final: 0.5980 (tm-30) REVERT: A 437 ASP cc_start: 0.6714 (m-30) cc_final: 0.6337 (m-30) REVERT: A 457 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7040 (ttmm) REVERT: A 499 LYS cc_start: 0.6928 (tttp) cc_final: 0.6322 (ttpp) REVERT: C 12 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.7035 (mtm) REVERT: C 106 LYS cc_start: 0.7142 (mttt) cc_final: 0.6833 (mttp) REVERT: C 107 THR cc_start: 0.7419 (m) cc_final: 0.6755 (t) REVERT: C 249 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6772 (t0) REVERT: C 437 ASP cc_start: 0.6712 (m-30) cc_final: 0.6334 (m-30) REVERT: C 457 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7037 (ttmm) REVERT: C 499 LYS cc_start: 0.6754 (tttp) cc_final: 0.6190 (ttpp) REVERT: D 12 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.7026 (mtm) REVERT: D 106 LYS cc_start: 0.7146 (mttt) cc_final: 0.6836 (mttp) REVERT: D 107 THR cc_start: 0.7421 (m) cc_final: 0.6768 (t) REVERT: D 119 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: D 424 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.5981 (tm-30) REVERT: D 437 ASP cc_start: 0.6717 (m-30) cc_final: 0.6339 (m-30) REVERT: D 457 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7030 (ttmm) REVERT: D 499 LYS cc_start: 0.6751 (tttp) cc_final: 0.6188 (ttpp) outliers start: 54 outliers final: 24 residues processed: 209 average time/residue: 1.5303 time to fit residues: 351.1245 Evaluate side-chains 193 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 201 SER 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 361 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 201 SER 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 361 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 457 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN A 226 ASN C 226 ASN D 226 ASN D 305 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16888 Z= 0.170 Angle : 0.545 6.941 23040 Z= 0.275 Chirality : 0.043 0.139 2328 Planarity : 0.004 0.041 3052 Dihedral : 8.711 127.611 2260 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.23 % Allowed : 14.54 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 1980 helix: 0.96 (0.20), residues: 676 sheet: 0.75 (0.33), residues: 276 loop : -0.32 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 183 HIS 0.003 0.001 HIS B 235 PHE 0.013 0.001 PHE D 409 TYR 0.015 0.001 TYR A 236 ARG 0.003 0.000 ARG D 363 *********************** 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 203 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 2.089 Fit side-chains REVERT: B 23 LYS cc_start: 0.7134 (pttm) cc_final: 0.6890 (ptmt) REVERT: B 106 LYS cc_start: 0.7144 (mttt) cc_final: 0.6854 (mttp) REVERT: B 107 THR cc_start: 0.7286 (m) cc_final: 0.6728 (t) REVERT: B 119 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6458 (mp0) REVERT: B 298 ASP cc_start: 0.7957 (t0) cc_final: 0.7594 (t0) REVERT: B 424 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.5877 (tm-30) REVERT: B 437 ASP cc_start: 0.6610 (m-30) cc_final: 0.6070 (m-30) REVERT: B 458 ARG cc_start: 0.7020 (mtp180) cc_final: 0.6600 (mtm180) REVERT: B 499 LYS cc_start: 0.6993 (tttp) cc_final: 0.6278 (ttpp) REVERT: A 23 LYS cc_start: 0.7124 (pttm) cc_final: 0.6922 (ptmt) REVERT: A 106 LYS cc_start: 0.7102 (mttt) cc_final: 0.6817 (mttp) REVERT: A 107 THR cc_start: 0.7287 (m) cc_final: 0.6731 (t) REVERT: A 249 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6646 (t0) REVERT: A 298 ASP cc_start: 0.7967 (t0) cc_final: 0.7607 (t0) REVERT: A 424 GLN cc_start: 0.6583 (OUTLIER) cc_final: 0.5878 (tm-30) REVERT: A 437 ASP cc_start: 0.6608 (m-30) cc_final: 0.6110 (m-30) REVERT: A 458 ARG cc_start: 0.7027 (mtp180) cc_final: 0.6604 (mtm180) REVERT: A 499 LYS cc_start: 0.7001 (tttp) cc_final: 0.6284 (ttpp) REVERT: C 23 LYS cc_start: 0.7088 (pttm) cc_final: 0.6879 (ptmt) REVERT: C 106 LYS cc_start: 0.7106 (mttt) cc_final: 0.6819 (mttp) REVERT: C 107 THR cc_start: 0.7288 (m) cc_final: 0.6732 (t) REVERT: C 249 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6647 (t0) REVERT: C 298 ASP cc_start: 0.7970 (t0) cc_final: 0.7614 (t0) REVERT: C 437 ASP cc_start: 0.6604 (m-30) cc_final: 0.6056 (m-30) REVERT: C 458 ARG cc_start: 0.6980 (mtp180) cc_final: 0.6561 (mtm180) REVERT: C 499 LYS cc_start: 0.7002 (tttp) cc_final: 0.6285 (ttpp) REVERT: D 106 LYS cc_start: 0.7106 (mttt) cc_final: 0.6820 (mttp) REVERT: D 107 THR cc_start: 0.7285 (m) cc_final: 0.6728 (t) REVERT: D 119 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6456 (mp0) REVERT: D 298 ASP cc_start: 0.7965 (t0) cc_final: 0.7601 (t0) REVERT: D 424 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.5878 (tm-30) REVERT: D 437 ASP cc_start: 0.6610 (m-30) cc_final: 0.6068 (m-30) REVERT: D 458 ARG cc_start: 0.6934 (mtm-85) cc_final: 0.6386 (mtm180) REVERT: D 499 LYS cc_start: 0.6994 (tttp) cc_final: 0.6279 (ttpp) outliers start: 21 outliers final: 11 residues processed: 200 average time/residue: 1.4986 time to fit residues: 334.3403 Evaluate side-chains 187 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 236 TYR 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 182 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN A 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16888 Z= 0.298 Angle : 0.616 8.428 23040 Z= 0.309 Chirality : 0.046 0.148 2328 Planarity : 0.005 0.043 3052 Dihedral : 9.311 134.881 2260 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.46 % Allowed : 14.37 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1980 helix: 0.84 (0.20), residues: 684 sheet: 0.57 (0.33), residues: 276 loop : -0.35 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 183 HIS 0.005 0.001 HIS A 235 PHE 0.015 0.002 PHE D 136 TYR 0.019 0.002 TYR A 236 ARG 0.003 0.000 ARG B 72 *********************** 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 188 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 2.539 Fit side-chains REVERT: B 106 LYS cc_start: 0.7094 (mttt) cc_final: 0.6818 (mttp) REVERT: B 107 THR cc_start: 0.7276 (m) cc_final: 0.6677 (t) REVERT: B 298 ASP cc_start: 0.7997 (t0) cc_final: 0.7661 (t0) REVERT: B 424 GLN cc_start: 0.6742 (OUTLIER) cc_final: 0.5990 (tm-30) REVERT: B 437 ASP cc_start: 0.6632 (m-30) cc_final: 0.6104 (m-30) REVERT: B 458 ARG cc_start: 0.6949 (ttp-170) cc_final: 0.6481 (mtm180) REVERT: B 499 LYS cc_start: 0.6930 (tttp) cc_final: 0.6299 (ttpp) REVERT: A 12 MET cc_start: 0.7242 (mtm) cc_final: 0.6913 (mtm) REVERT: A 106 LYS cc_start: 0.7091 (mttt) cc_final: 0.6810 (mttp) REVERT: A 107 THR cc_start: 0.7280 (m) cc_final: 0.6678 (t) REVERT: A 249 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6660 (t0) REVERT: A 298 ASP cc_start: 0.8004 (t0) cc_final: 0.7675 (t0) REVERT: A 424 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.5988 (tm-30) REVERT: A 437 ASP cc_start: 0.6631 (m-30) cc_final: 0.6136 (m-30) REVERT: A 458 ARG cc_start: 0.6947 (ttp-170) cc_final: 0.6479 (mtm180) REVERT: A 499 LYS cc_start: 0.6959 (tttp) cc_final: 0.6318 (ttpp) REVERT: C 23 LYS cc_start: 0.7081 (pttm) cc_final: 0.6872 (ptmt) REVERT: C 106 LYS cc_start: 0.7092 (mttt) cc_final: 0.6812 (mttp) REVERT: C 107 THR cc_start: 0.7280 (m) cc_final: 0.6680 (t) REVERT: C 249 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6663 (t0) REVERT: C 298 ASP cc_start: 0.8004 (t0) cc_final: 0.7680 (t0) REVERT: C 437 ASP cc_start: 0.6683 (m-30) cc_final: 0.6247 (m-30) REVERT: C 458 ARG cc_start: 0.6922 (ttp-170) cc_final: 0.6456 (mtm180) REVERT: C 499 LYS cc_start: 0.6960 (tttp) cc_final: 0.6320 (ttpp) REVERT: D 106 LYS cc_start: 0.7099 (mttt) cc_final: 0.6824 (mttp) REVERT: D 107 THR cc_start: 0.7281 (m) cc_final: 0.6685 (t) REVERT: D 298 ASP cc_start: 0.7996 (t0) cc_final: 0.7668 (t0) REVERT: D 424 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.5990 (tm-30) REVERT: D 437 ASP cc_start: 0.6633 (m-30) cc_final: 0.6092 (m-30) REVERT: D 458 ARG cc_start: 0.6875 (mtm-85) cc_final: 0.6402 (mtm180) REVERT: D 499 LYS cc_start: 0.6931 (tttp) cc_final: 0.6300 (ttpp) outliers start: 25 outliers final: 16 residues processed: 179 average time/residue: 1.5365 time to fit residues: 302.9241 Evaluate side-chains 183 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 SER 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 201 SER 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 201 SER 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 D residue 201 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 120 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN A 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16888 Z= 0.268 Angle : 0.599 8.804 23040 Z= 0.301 Chirality : 0.045 0.147 2328 Planarity : 0.005 0.045 3052 Dihedral : 9.268 136.066 2260 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.99 % Allowed : 13.67 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 1980 helix: 0.87 (0.20), residues: 684 sheet: 0.52 (0.33), residues: 276 loop : -0.31 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 183 HIS 0.004 0.001 HIS D 235 PHE 0.014 0.002 PHE D 136 TYR 0.018 0.002 TYR B 236 ARG 0.003 0.000 ARG D 72 *********************** 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 198 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 1.906 Fit side-chains REVERT: B 12 MET cc_start: 0.7269 (mtm) cc_final: 0.6945 (mtm) REVERT: B 23 LYS cc_start: 0.7202 (pttm) cc_final: 0.6945 (ptmt) REVERT: B 101 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7068 (tp30) REVERT: B 106 LYS cc_start: 0.7083 (mttt) cc_final: 0.6808 (mttp) REVERT: B 107 THR cc_start: 0.7227 (m) cc_final: 0.6649 (t) REVERT: B 119 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6456 (mp0) REVERT: B 191 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: B 249 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6687 (t0) REVERT: B 298 ASP cc_start: 0.7934 (t0) cc_final: 0.7620 (t0) REVERT: B 424 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.5990 (tm-30) REVERT: B 437 ASP cc_start: 0.6634 (m-30) cc_final: 0.6133 (m-30) REVERT: B 458 ARG cc_start: 0.6995 (ttp-170) cc_final: 0.6556 (mtm180) REVERT: B 499 LYS cc_start: 0.6950 (tttp) cc_final: 0.6257 (ttpp) REVERT: A 12 MET cc_start: 0.7269 (mtm) cc_final: 0.6919 (mtm) REVERT: A 23 LYS cc_start: 0.7176 (pttm) cc_final: 0.6929 (ptmt) REVERT: A 106 LYS cc_start: 0.7075 (mttt) cc_final: 0.6808 (mttp) REVERT: A 107 THR cc_start: 0.7232 (m) cc_final: 0.6654 (t) REVERT: A 191 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: A 249 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6676 (t0) REVERT: A 298 ASP cc_start: 0.7942 (t0) cc_final: 0.7634 (t0) REVERT: A 424 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.5983 (tm-30) REVERT: A 437 ASP cc_start: 0.6633 (m-30) cc_final: 0.6129 (m-30) REVERT: A 458 ARG cc_start: 0.6997 (ttp-170) cc_final: 0.6535 (mtm180) REVERT: A 499 LYS cc_start: 0.6966 (tttp) cc_final: 0.6317 (ttpp) REVERT: C 12 MET cc_start: 0.7312 (mtm) cc_final: 0.6951 (mtm) REVERT: C 23 LYS cc_start: 0.7017 (pttm) cc_final: 0.6807 (ptmt) REVERT: C 101 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6963 (tp30) REVERT: C 106 LYS cc_start: 0.7078 (mttt) cc_final: 0.6810 (mttp) REVERT: C 107 THR cc_start: 0.7233 (m) cc_final: 0.6655 (t) REVERT: C 191 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: C 249 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6677 (t0) REVERT: C 298 ASP cc_start: 0.7941 (t0) cc_final: 0.7640 (t0) REVERT: C 437 ASP cc_start: 0.6688 (m-30) cc_final: 0.6247 (m-30) REVERT: C 458 ARG cc_start: 0.6997 (ttp-170) cc_final: 0.6536 (mtm180) REVERT: C 499 LYS cc_start: 0.6959 (tttp) cc_final: 0.6311 (ttpp) REVERT: D 12 MET cc_start: 0.7258 (mtm) cc_final: 0.6927 (mtm) REVERT: D 23 LYS cc_start: 0.7170 (pttm) cc_final: 0.6924 (ptmt) REVERT: D 106 LYS cc_start: 0.7089 (mttt) cc_final: 0.6814 (mttp) REVERT: D 107 THR cc_start: 0.7302 (m) cc_final: 0.6724 (t) REVERT: D 119 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6467 (mp0) REVERT: D 191 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: D 249 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6691 (t0) REVERT: D 298 ASP cc_start: 0.8005 (t0) cc_final: 0.7672 (t0) REVERT: D 424 GLN cc_start: 0.6735 (OUTLIER) cc_final: 0.5983 (tm-30) REVERT: D 437 ASP cc_start: 0.6635 (m-30) cc_final: 0.6132 (m-30) REVERT: D 458 ARG cc_start: 0.6881 (mtm-85) cc_final: 0.6414 (mtm180) REVERT: D 499 LYS cc_start: 0.6949 (tttp) cc_final: 0.6258 (ttpp) outliers start: 34 outliers final: 16 residues processed: 190 average time/residue: 1.5192 time to fit residues: 318.0515 Evaluate side-chains 194 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 201 SER 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 191 GLU Chi-restraints excluded: chain A residue 201 SER 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 191 GLU Chi-restraints excluded: chain C residue 201 SER 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 D residue 191 GLU Chi-restraints excluded: chain D residue 201 SER 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 171 optimal weight: 8.9990 chunk 180 optimal weight: 0.2980 chunk 165 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN A 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16888 Z= 0.161 Angle : 0.535 8.186 23040 Z= 0.267 Chirality : 0.043 0.136 2328 Planarity : 0.004 0.042 3052 Dihedral : 8.462 129.124 2260 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.29 % Allowed : 14.37 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1980 helix: 1.15 (0.20), residues: 680 sheet: 0.64 (0.33), residues: 276 loop : -0.16 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 183 HIS 0.003 0.001 HIS B 235 PHE 0.011 0.001 PHE B 136 TYR 0.015 0.001 TYR B 236 ARG 0.003 0.000 ARG B 382 *********************** 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 208 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 1.995 Fit side-chains REVERT: B 12 MET cc_start: 0.7221 (mtm) cc_final: 0.6917 (mtm) REVERT: B 23 LYS cc_start: 0.7165 (pttm) cc_final: 0.6948 (ptmt) REVERT: B 106 LYS cc_start: 0.7059 (mttt) cc_final: 0.6795 (mttp) REVERT: B 107 THR cc_start: 0.7294 (m) cc_final: 0.6754 (t) REVERT: B 119 GLU cc_start: 0.6659 (mt-10) cc_final: 0.6361 (mp0) REVERT: B 124 ASP cc_start: 0.7262 (t0) cc_final: 0.7003 (t0) REVERT: B 298 ASP cc_start: 0.7988 (t0) cc_final: 0.7642 (t0) REVERT: B 424 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.5927 (tm-30) REVERT: B 437 ASP cc_start: 0.6597 (m-30) cc_final: 0.6072 (m-30) REVERT: B 458 ARG cc_start: 0.7018 (ttp-170) cc_final: 0.6566 (mtm180) REVERT: B 499 LYS cc_start: 0.6930 (tttp) cc_final: 0.6243 (ttpp) REVERT: A 12 MET cc_start: 0.7277 (mtm) cc_final: 0.6936 (mtm) REVERT: A 23 LYS cc_start: 0.7170 (pttm) cc_final: 0.6953 (ptmt) REVERT: A 106 LYS cc_start: 0.7100 (mttt) cc_final: 0.6836 (mttp) REVERT: A 107 THR cc_start: 0.7273 (m) cc_final: 0.6727 (t) REVERT: A 249 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6676 (t0) REVERT: A 298 ASP cc_start: 0.7996 (t0) cc_final: 0.7651 (t0) REVERT: A 424 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.5919 (tm-30) REVERT: A 437 ASP cc_start: 0.6594 (m-30) cc_final: 0.6066 (m-30) REVERT: A 458 ARG cc_start: 0.6970 (ttp-170) cc_final: 0.6530 (mtm180) REVERT: A 499 LYS cc_start: 0.6930 (tttp) cc_final: 0.6235 (ttpp) REVERT: C 12 MET cc_start: 0.7277 (mtm) cc_final: 0.6949 (mtm) REVERT: C 23 LYS cc_start: 0.7079 (pttm) cc_final: 0.6875 (ptmt) REVERT: C 106 LYS cc_start: 0.7103 (mttt) cc_final: 0.6838 (mttp) REVERT: C 107 THR cc_start: 0.7271 (m) cc_final: 0.6726 (t) REVERT: C 249 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.6677 (t0) REVERT: C 298 ASP cc_start: 0.7994 (t0) cc_final: 0.7658 (t0) REVERT: C 437 ASP cc_start: 0.6600 (m-30) cc_final: 0.6051 (m-30) REVERT: C 458 ARG cc_start: 0.6978 (ttp-170) cc_final: 0.6534 (mtm180) REVERT: C 499 LYS cc_start: 0.6938 (tttp) cc_final: 0.6250 (ttpp) REVERT: D 12 MET cc_start: 0.7225 (mtm) cc_final: 0.6921 (mtm) REVERT: D 23 LYS cc_start: 0.7168 (pttm) cc_final: 0.6952 (ptmt) REVERT: D 106 LYS cc_start: 0.7064 (mttt) cc_final: 0.6800 (mttp) REVERT: D 107 THR cc_start: 0.7271 (m) cc_final: 0.6723 (t) REVERT: D 119 GLU cc_start: 0.6658 (mt-10) cc_final: 0.6361 (mp0) REVERT: D 124 ASP cc_start: 0.7259 (t0) cc_final: 0.7000 (t0) REVERT: D 298 ASP cc_start: 0.7986 (t0) cc_final: 0.7648 (t0) REVERT: D 424 GLN cc_start: 0.6678 (OUTLIER) cc_final: 0.5920 (tm-30) REVERT: D 437 ASP cc_start: 0.6596 (m-30) cc_final: 0.6070 (m-30) REVERT: D 499 LYS cc_start: 0.6930 (tttp) cc_final: 0.6243 (ttpp) outliers start: 22 outliers final: 13 residues processed: 202 average time/residue: 1.4109 time to fit residues: 318.0250 Evaluate side-chains 195 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 236 TYR 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 115 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 88 optimal weight: 0.0470 chunk 129 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN A 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16888 Z= 0.191 Angle : 0.556 10.575 23040 Z= 0.277 Chirality : 0.043 0.148 2328 Planarity : 0.004 0.044 3052 Dihedral : 8.675 129.995 2260 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.29 % Allowed : 14.72 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 1980 helix: 1.18 (0.20), residues: 680 sheet: 0.64 (0.33), residues: 276 loop : -0.17 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 183 HIS 0.004 0.001 HIS A 364 PHE 0.013 0.001 PHE D 136 TYR 0.017 0.001 TYR A 236 ARG 0.003 0.000 ARG D 382 ********************** 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 192 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 1.878 Fit side-chains REVERT: B 12 MET cc_start: 0.7204 (mtm) cc_final: 0.6926 (mtm) REVERT: B 23 LYS cc_start: 0.7158 (pttm) cc_final: 0.6945 (ptmt) REVERT: B 106 LYS cc_start: 0.7062 (mttt) cc_final: 0.6793 (mttp) REVERT: B 107 THR cc_start: 0.7285 (m) cc_final: 0.6711 (t) REVERT: B 119 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6377 (mp0) REVERT: B 298 ASP cc_start: 0.7987 (t0) cc_final: 0.7661 (t0) REVERT: B 424 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.5941 (tm-30) REVERT: B 437 ASP cc_start: 0.6599 (m-30) cc_final: 0.6045 (m-30) REVERT: B 458 ARG cc_start: 0.6993 (ttp-170) cc_final: 0.6527 (mtm180) REVERT: B 499 LYS cc_start: 0.6963 (tttp) cc_final: 0.6272 (ttpp) REVERT: A 12 MET cc_start: 0.7255 (mtm) cc_final: 0.6927 (mtm) REVERT: A 23 LYS cc_start: 0.7160 (pttm) cc_final: 0.6948 (ptmt) REVERT: A 106 LYS cc_start: 0.7108 (mttt) cc_final: 0.6839 (mttp) REVERT: A 107 THR cc_start: 0.7286 (m) cc_final: 0.6713 (t) REVERT: A 249 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6702 (t0) REVERT: A 298 ASP cc_start: 0.7997 (t0) cc_final: 0.7675 (t0) REVERT: A 424 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.5932 (tm-30) REVERT: A 437 ASP cc_start: 0.6598 (m-30) cc_final: 0.6042 (m-30) REVERT: A 458 ARG cc_start: 0.6994 (ttp-170) cc_final: 0.6528 (mtm180) REVERT: A 499 LYS cc_start: 0.6971 (tttp) cc_final: 0.6279 (ttpp) REVERT: C 12 MET cc_start: 0.7267 (mtm) cc_final: 0.6939 (mtm) REVERT: C 23 LYS cc_start: 0.7076 (pttm) cc_final: 0.6871 (ptmt) REVERT: C 106 LYS cc_start: 0.7110 (mttt) cc_final: 0.6841 (mttp) REVERT: C 107 THR cc_start: 0.7287 (m) cc_final: 0.6712 (t) REVERT: C 249 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6707 (t0) REVERT: C 298 ASP cc_start: 0.7921 (t0) cc_final: 0.7635 (t0) REVERT: C 437 ASP cc_start: 0.6648 (m-30) cc_final: 0.6206 (m-30) REVERT: C 458 ARG cc_start: 0.6982 (ttp-170) cc_final: 0.6537 (mtm180) REVERT: C 499 LYS cc_start: 0.6973 (tttp) cc_final: 0.6281 (ttpp) REVERT: D 12 MET cc_start: 0.7206 (mtm) cc_final: 0.6928 (mtm) REVERT: D 23 LYS cc_start: 0.7161 (pttm) cc_final: 0.6950 (ptmt) REVERT: D 101 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7037 (tp30) REVERT: D 106 LYS cc_start: 0.7064 (mttt) cc_final: 0.6797 (mttp) REVERT: D 107 THR cc_start: 0.7286 (m) cc_final: 0.6712 (t) REVERT: D 119 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6376 (mp0) REVERT: D 191 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6972 (pm20) REVERT: D 298 ASP cc_start: 0.7987 (t0) cc_final: 0.7666 (t0) REVERT: D 424 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.5934 (tm-30) REVERT: D 437 ASP cc_start: 0.6598 (m-30) cc_final: 0.6053 (m-30) REVERT: D 458 ARG cc_start: 0.6969 (mtp180) cc_final: 0.6634 (mtm180) REVERT: D 499 LYS cc_start: 0.6963 (tttp) cc_final: 0.6273 (ttpp) outliers start: 22 outliers final: 13 residues processed: 190 average time/residue: 1.4314 time to fit residues: 300.3558 Evaluate side-chains 191 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 236 TYR 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 123 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN A 226 ASN C 102 HIS C 226 ASN D 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.113554 restraints weight = 18826.479| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.27 r_work: 0.3149 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16888 Z= 0.158 Angle : 0.531 9.604 23040 Z= 0.264 Chirality : 0.043 0.144 2328 Planarity : 0.004 0.042 3052 Dihedral : 8.239 124.807 2260 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.23 % Allowed : 14.66 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 1980 helix: 1.31 (0.20), residues: 680 sheet: 0.71 (0.33), residues: 276 loop : -0.12 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 183 HIS 0.005 0.001 HIS C 102 PHE 0.011 0.001 PHE A 136 TYR 0.015 0.001 TYR A 236 ARG 0.004 0.000 ARG D 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5663.39 seconds wall clock time: 103 minutes 9.08 seconds (6189.08 seconds total)