Starting phenix.real_space_refine on Tue Jan 21 06:39:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wzj_37954/01_2025/8wzj_37954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wzj_37954/01_2025/8wzj_37954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wzj_37954/01_2025/8wzj_37954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wzj_37954/01_2025/8wzj_37954.map" model { file = "/net/cci-nas-00/data/ceres_data/8wzj_37954/01_2025/8wzj_37954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wzj_37954/01_2025/8wzj_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 8.38, per 1000 atoms: 0.51 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: 3.94 Conformation dependent library (CDL) restraints added in 2.3 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: 2.02 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: 4.61 Time building geometry restraints manager: 4.56 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.690 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: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 35.580 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.920 ------------------------------------------------------------------------------- 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 : 1.814 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: 1.6991 time to fit residues: 592.2686 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 : 1.772 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111074 restraints weight = 18918.319| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.27 r_work: 0.3121 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 1.804 Fit side-chains REVERT: B 19 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6782 (ttm-80) REVERT: B 389 ASP cc_start: 0.6965 (OUTLIER) cc_final: 0.6402 (m-30) REVERT: B 476 LYS cc_start: 0.8168 (mttp) cc_final: 0.7949 (mtpp) REVERT: B 499 LYS cc_start: 0.7682 (tttp) cc_final: 0.7169 (ttpp) REVERT: A 19 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6771 (ttm-80) REVERT: A 107 THR cc_start: 0.8105 (m) cc_final: 0.7745 (t) REVERT: A 389 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6526 (m-30) REVERT: A 476 LYS cc_start: 0.8167 (mttp) cc_final: 0.7963 (mtpp) REVERT: A 499 LYS cc_start: 0.7678 (tttp) cc_final: 0.7157 (ttpp) REVERT: C 19 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6781 (ttm-80) REVERT: C 107 THR cc_start: 0.8106 (m) cc_final: 0.7752 (t) REVERT: C 389 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6521 (m-30) REVERT: C 476 LYS cc_start: 0.8128 (mttp) cc_final: 0.7914 (mtpp) REVERT: C 499 LYS cc_start: 0.7626 (tttp) cc_final: 0.7148 (ttpp) REVERT: D 19 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.6789 (ttm-80) REVERT: D 389 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6399 (m-30) REVERT: D 499 LYS cc_start: 0.7631 (tttp) cc_final: 0.7153 (ttpp) outliers start: 26 outliers final: 8 residues processed: 212 average time/residue: 1.4124 time to fit residues: 330.3936 Evaluate side-chains 165 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 32 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 B 369 ASN A 63 HIS A 102 HIS A 226 ASN A 338 ASN A 369 ASN C 63 HIS C 102 HIS C 226 ASN C 338 ASN C 369 ASN D 63 HIS D 226 ASN D 338 ASN D 369 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104873 restraints weight = 19063.830| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.33 r_work: 0.3022 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 16888 Z= 0.411 Angle : 0.689 7.761 23040 Z= 0.349 Chirality : 0.049 0.153 2328 Planarity : 0.005 0.041 3052 Dihedral : 9.682 134.855 2260 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.43 % Favored : 96.36 % Rotamer: Outliers : 2.57 % Allowed : 11.16 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.20), residues: 684 sheet: 0.54 (0.32), residues: 272 loop : -0.40 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 183 HIS 0.007 0.002 HIS D 372 PHE 0.015 0.003 PHE B 185 TYR 0.021 0.002 TYR A 236 ARG 0.004 0.001 ARG B 365 *********************** 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 208 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 1.758 Fit side-chains REVERT: B 12 MET cc_start: 0.8642 (mtm) cc_final: 0.8272 (mtm) REVERT: B 19 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.6979 (ttm-80) REVERT: B 101 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: B 107 THR cc_start: 0.8256 (m) cc_final: 0.7859 (t) REVERT: B 424 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6808 (tm-30) REVERT: B 437 ASP cc_start: 0.7402 (m-30) cc_final: 0.6820 (m-30) REVERT: B 499 LYS cc_start: 0.7762 (tttp) cc_final: 0.7241 (ttpp) REVERT: A 12 MET cc_start: 0.8648 (mtm) cc_final: 0.8222 (mtm) REVERT: A 19 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6942 (ttm-80) REVERT: A 101 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7597 (tp30) REVERT: A 107 THR cc_start: 0.8269 (m) cc_final: 0.7858 (t) REVERT: A 424 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6799 (tm-30) REVERT: A 437 ASP cc_start: 0.7390 (m-30) cc_final: 0.6820 (m-30) REVERT: A 499 LYS cc_start: 0.7744 (tttp) cc_final: 0.7242 (ttpp) REVERT: C 12 MET cc_start: 0.8647 (mtm) cc_final: 0.8257 (mtm) REVERT: C 19 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.6941 (ttm-80) REVERT: C 101 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7602 (tp30) REVERT: C 107 THR cc_start: 0.8251 (m) cc_final: 0.7848 (t) REVERT: C 437 ASP cc_start: 0.7377 (m-30) cc_final: 0.6997 (m-30) REVERT: C 499 LYS cc_start: 0.7744 (tttp) cc_final: 0.7246 (ttpp) REVERT: D 12 MET cc_start: 0.8653 (mtm) cc_final: 0.8285 (mtm) REVERT: D 19 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.6988 (ttm-80) REVERT: D 101 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7595 (tp30) REVERT: D 107 THR cc_start: 0.8258 (m) cc_final: 0.7850 (t) REVERT: D 424 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6807 (tm-30) REVERT: D 437 ASP cc_start: 0.7387 (m-30) cc_final: 0.6817 (m-30) REVERT: D 499 LYS cc_start: 0.7766 (tttp) cc_final: 0.7245 (ttpp) outliers start: 44 outliers final: 18 residues processed: 196 average time/residue: 1.4539 time to fit residues: 314.7228 Evaluate side-chains 173 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 189 optimal weight: 0.1980 chunk 100 optimal weight: 3.9990 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 226 ASN A 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.129210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.109276 restraints weight = 18828.648| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.27 r_work: 0.3096 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2651 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= 0.206 Angle : 0.554 6.773 23040 Z= 0.280 Chirality : 0.044 0.142 2328 Planarity : 0.004 0.042 3052 Dihedral : 8.750 122.986 2260 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.87 % Allowed : 12.79 % Favored : 85.34 % 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: 0.41 (0.19), residues: 1980 helix: 0.98 (0.20), residues: 684 sheet: 0.65 (0.33), residues: 276 loop : -0.25 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 183 HIS 0.003 0.001 HIS C 235 PHE 0.012 0.002 PHE B 409 TYR 0.016 0.001 TYR B 236 ARG 0.003 0.000 ARG C 363 *********************** 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 196 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 1.896 Fit side-chains REVERT: B 101 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7208 (tp30) REVERT: B 107 THR cc_start: 0.8172 (m) cc_final: 0.7823 (t) REVERT: B 249 ASP cc_start: 0.7741 (m-30) cc_final: 0.7423 (t0) REVERT: B 424 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: B 437 ASP cc_start: 0.7392 (m-30) cc_final: 0.6797 (m-30) REVERT: B 499 LYS cc_start: 0.7711 (tttp) cc_final: 0.7198 (ttpp) REVERT: A 59 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8073 (t0) REVERT: A 107 THR cc_start: 0.8165 (m) cc_final: 0.7817 (t) REVERT: A 249 ASP cc_start: 0.7748 (m-30) cc_final: 0.7434 (t0) REVERT: A 424 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6719 (tm-30) REVERT: A 437 ASP cc_start: 0.7383 (m-30) cc_final: 0.6783 (m-30) REVERT: A 499 LYS cc_start: 0.7691 (tttp) cc_final: 0.7198 (ttpp) REVERT: C 59 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8093 (t0) REVERT: C 101 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7224 (tp30) REVERT: C 107 THR cc_start: 0.8193 (m) cc_final: 0.7835 (t) REVERT: C 249 ASP cc_start: 0.7765 (m-30) cc_final: 0.7448 (t0) REVERT: C 437 ASP cc_start: 0.7373 (m-30) cc_final: 0.6762 (m-30) REVERT: C 499 LYS cc_start: 0.7706 (tttp) cc_final: 0.7205 (ttpp) REVERT: D 101 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7207 (tp30) REVERT: D 107 THR cc_start: 0.8200 (m) cc_final: 0.7840 (t) REVERT: D 424 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6689 (tm-30) REVERT: D 437 ASP cc_start: 0.7381 (m-30) cc_final: 0.6766 (m-30) REVERT: D 499 LYS cc_start: 0.7694 (tttp) cc_final: 0.7183 (ttpp) outliers start: 32 outliers final: 16 residues processed: 188 average time/residue: 1.4490 time to fit residues: 301.2838 Evaluate side-chains 177 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 159 optimal weight: 0.4980 chunk 186 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111641 restraints weight = 19104.518| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.28 r_work: 0.3130 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16888 Z= 0.161 Angle : 0.522 6.598 23040 Z= 0.261 Chirality : 0.043 0.134 2328 Planarity : 0.004 0.042 3052 Dihedral : 8.104 114.294 2260 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.28 % Allowed : 12.73 % Favored : 84.99 % 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: 1.23 (0.20), residues: 684 sheet: 0.67 (0.33), residues: 276 loop : -0.16 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 183 HIS 0.004 0.001 HIS C 235 PHE 0.011 0.001 PHE D 136 TYR 0.016 0.001 TYR B 236 ARG 0.003 0.000 ARG D 382 *********************** 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 220 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 1.585 Fit side-chains REVERT: B 107 THR cc_start: 0.8173 (m) cc_final: 0.7813 (t) REVERT: B 191 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: B 249 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7502 (t0) REVERT: B 424 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6716 (tm-30) REVERT: B 437 ASP cc_start: 0.7339 (m-30) cc_final: 0.6724 (m-30) REVERT: B 499 LYS cc_start: 0.7741 (tttp) cc_final: 0.7201 (ttpp) REVERT: A 59 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7969 (t0) REVERT: A 107 THR cc_start: 0.8179 (m) cc_final: 0.7830 (t) REVERT: A 191 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7824 (pm20) REVERT: A 249 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7484 (t0) REVERT: A 424 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: A 437 ASP cc_start: 0.7313 (m-30) cc_final: 0.6705 (m-30) REVERT: A 499 LYS cc_start: 0.7754 (tttp) cc_final: 0.7210 (ttpp) REVERT: C 59 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7983 (t0) REVERT: C 101 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: C 107 THR cc_start: 0.8169 (m) cc_final: 0.7813 (t) REVERT: C 191 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: C 249 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7526 (t0) REVERT: C 437 ASP cc_start: 0.7335 (m-30) cc_final: 0.6676 (m-30) REVERT: C 499 LYS cc_start: 0.7778 (tttp) cc_final: 0.7223 (ttpp) REVERT: D 107 THR cc_start: 0.8172 (m) cc_final: 0.7813 (t) REVERT: D 191 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7826 (pm20) REVERT: D 249 ASP cc_start: 0.7772 (m-30) cc_final: 0.7481 (t0) REVERT: D 424 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6711 (tm-30) REVERT: D 437 ASP cc_start: 0.7330 (m-30) cc_final: 0.6715 (m-30) REVERT: D 499 LYS cc_start: 0.7754 (tttp) cc_final: 0.7193 (ttpp) outliers start: 39 outliers final: 15 residues processed: 209 average time/residue: 1.2696 time to fit residues: 296.0822 Evaluate side-chains 193 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 191 GLU 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 59 ASP Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 191 GLU 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 150 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 191 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 61 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS B 226 ASN B 439 ASN A 226 ASN A 439 ASN C 226 ASN C 439 ASN D 102 HIS D 226 ASN D 439 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.132286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.112630 restraints weight = 18898.370| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.27 r_work: 0.3146 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16888 Z= 0.161 Angle : 0.517 6.496 23040 Z= 0.257 Chirality : 0.043 0.132 2328 Planarity : 0.004 0.042 3052 Dihedral : 7.916 108.117 2260 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.22 % Allowed : 12.56 % Favored : 85.22 % 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: 0.67 (0.19), residues: 1980 helix: 1.27 (0.20), residues: 688 sheet: 0.68 (0.33), residues: 276 loop : -0.13 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 183 HIS 0.003 0.001 HIS B 102 PHE 0.012 0.001 PHE C 136 TYR 0.015 0.001 TYR B 236 ARG 0.003 0.000 ARG D 382 *********************** 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 207 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.900 Fit side-chains REVERT: B 12 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8125 (mtm) REVERT: B 101 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7248 (tp30) REVERT: B 107 THR cc_start: 0.8169 (m) cc_final: 0.7815 (t) REVERT: B 191 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: B 249 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7491 (t0) REVERT: B 424 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6682 (tm-30) REVERT: B 437 ASP cc_start: 0.7362 (m-30) cc_final: 0.6736 (m-30) REVERT: B 458 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7832 (mtm180) REVERT: B 499 LYS cc_start: 0.7716 (tttp) cc_final: 0.7155 (ttpp) REVERT: A 12 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8108 (mtm) REVERT: A 107 THR cc_start: 0.8157 (m) cc_final: 0.7810 (t) REVERT: A 191 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: A 249 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7454 (t0) REVERT: A 424 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: A 437 ASP cc_start: 0.7335 (m-30) cc_final: 0.6671 (m-30) REVERT: A 499 LYS cc_start: 0.7714 (tttp) cc_final: 0.7160 (ttpp) REVERT: C 101 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7219 (tp30) REVERT: C 107 THR cc_start: 0.8150 (m) cc_final: 0.7802 (t) REVERT: C 191 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7810 (pm20) REVERT: C 249 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7447 (t0) REVERT: C 424 GLN cc_start: 0.7755 (tp40) cc_final: 0.7425 (tm-30) REVERT: C 437 ASP cc_start: 0.7331 (m-30) cc_final: 0.6890 (m-30) REVERT: C 458 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7837 (mtm180) REVERT: C 499 LYS cc_start: 0.7718 (tttp) cc_final: 0.7162 (ttpp) REVERT: D 12 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8157 (mtm) REVERT: D 101 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7266 (tp30) REVERT: D 107 THR cc_start: 0.8166 (m) cc_final: 0.7815 (t) REVERT: D 191 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: D 249 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7429 (t0) REVERT: D 424 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6647 (tm-30) REVERT: D 437 ASP cc_start: 0.7348 (m-30) cc_final: 0.6699 (m-30) REVERT: D 499 LYS cc_start: 0.7719 (tttp) cc_final: 0.7148 (ttpp) outliers start: 38 outliers final: 19 residues processed: 195 average time/residue: 1.3952 time to fit residues: 301.0438 Evaluate side-chains 194 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 150 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 191 GLU 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 59 ASP 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 191 GLU 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 12 MET Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 8 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS B 226 ASN B 338 ASN A 102 HIS A 226 ASN A 338 ASN C 102 HIS C 226 ASN C 338 ASN D 102 HIS D 226 ASN D 338 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111388 restraints weight = 19021.766| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.32 r_work: 0.3124 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16888 Z= 0.181 Angle : 0.531 6.528 23040 Z= 0.264 Chirality : 0.043 0.134 2328 Planarity : 0.004 0.042 3052 Dihedral : 7.953 105.360 2260 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.57 % Allowed : 12.68 % Favored : 84.75 % 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: 0.66 (0.19), residues: 1980 helix: 1.29 (0.20), residues: 684 sheet: 0.67 (0.33), residues: 276 loop : -0.15 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 183 HIS 0.004 0.001 HIS D 102 PHE 0.012 0.001 PHE C 136 TYR 0.016 0.001 TYR D 236 ARG 0.003 0.000 ARG D 382 *********************** 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 217 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 1.837 Fit side-chains REVERT: B 12 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8124 (mtm) REVERT: B 59 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8072 (t0) REVERT: B 101 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: B 107 THR cc_start: 0.8207 (m) cc_final: 0.7854 (t) REVERT: B 191 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7810 (pm20) REVERT: B 249 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7442 (t0) REVERT: B 424 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6775 (tm-30) REVERT: B 437 ASP cc_start: 0.7387 (m-30) cc_final: 0.6698 (m-30) REVERT: B 458 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7836 (mtm180) REVERT: B 499 LYS cc_start: 0.7691 (tttp) cc_final: 0.7126 (ttpp) REVERT: A 12 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8141 (mtm) REVERT: A 59 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7974 (t0) REVERT: A 107 THR cc_start: 0.8195 (m) cc_final: 0.7845 (t) REVERT: A 191 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: A 249 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7476 (t0) REVERT: A 424 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: A 437 ASP cc_start: 0.7354 (m-30) cc_final: 0.6637 (m-30) REVERT: A 499 LYS cc_start: 0.7671 (tttp) cc_final: 0.7127 (ttpp) REVERT: C 12 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8211 (mtm) REVERT: C 101 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7306 (tp30) REVERT: C 107 THR cc_start: 0.8186 (m) cc_final: 0.7836 (t) REVERT: C 191 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: C 249 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7509 (t0) REVERT: C 424 GLN cc_start: 0.7693 (tp40) cc_final: 0.7356 (tm-30) REVERT: C 437 ASP cc_start: 0.7343 (m-30) cc_final: 0.6810 (m-30) REVERT: C 458 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.7843 (mtm180) REVERT: C 499 LYS cc_start: 0.7692 (tttp) cc_final: 0.7145 (ttpp) REVERT: D 59 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.8055 (t0) REVERT: D 101 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7304 (tp30) REVERT: D 107 THR cc_start: 0.8201 (m) cc_final: 0.7844 (t) REVERT: D 191 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7829 (pm20) REVERT: D 249 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7461 (t0) REVERT: D 424 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: D 437 ASP cc_start: 0.7370 (m-30) cc_final: 0.6651 (m-30) REVERT: D 499 LYS cc_start: 0.7671 (tttp) cc_final: 0.7110 (ttpp) outliers start: 44 outliers final: 18 residues processed: 205 average time/residue: 1.3929 time to fit residues: 316.0059 Evaluate side-chains 206 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 191 GLU 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 12 MET 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 191 GLU 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 59 ASP 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 191 GLU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 126 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS B 226 ASN B 338 ASN A 102 HIS A 226 ASN A 338 ASN C 102 HIS C 226 ASN C 338 ASN D 102 HIS D 226 ASN D 338 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.108998 restraints weight = 18992.519| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.33 r_work: 0.3095 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16888 Z= 0.234 Angle : 0.573 8.667 23040 Z= 0.286 Chirality : 0.044 0.139 2328 Planarity : 0.004 0.043 3052 Dihedral : 8.318 108.805 2260 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.57 % Allowed : 12.44 % Favored : 84.99 % 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: 1.14 (0.20), residues: 684 sheet: 0.56 (0.33), residues: 276 loop : -0.13 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 183 HIS 0.004 0.001 HIS A 102 PHE 0.014 0.002 PHE C 136 TYR 0.018 0.002 TYR A 236 ARG 0.003 0.000 ARG D 382 *********************** 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 224 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 2.076 Fit side-chains REVERT: B 59 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8150 (t0) REVERT: B 101 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7309 (tp30) REVERT: B 107 THR cc_start: 0.8202 (m) cc_final: 0.7859 (t) REVERT: B 191 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7692 (pm20) REVERT: B 249 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7432 (t0) REVERT: B 424 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6761 (tm-30) REVERT: B 437 ASP cc_start: 0.7411 (m-30) cc_final: 0.6894 (m-30) REVERT: B 458 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7859 (mtm180) REVERT: B 499 LYS cc_start: 0.7677 (tttp) cc_final: 0.7153 (ttpp) REVERT: A 59 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8125 (t0) REVERT: A 107 THR cc_start: 0.8200 (m) cc_final: 0.7856 (t) REVERT: A 191 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: A 249 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7454 (t0) REVERT: A 424 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6760 (tm-30) REVERT: A 437 ASP cc_start: 0.7397 (m-30) cc_final: 0.6867 (m-30) REVERT: A 458 ARG cc_start: 0.8238 (mtp180) cc_final: 0.7916 (mtm180) REVERT: A 499 LYS cc_start: 0.7661 (tttp) cc_final: 0.7151 (ttpp) REVERT: C 12 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8248 (mtm) REVERT: C 101 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: C 107 THR cc_start: 0.8189 (m) cc_final: 0.7843 (t) REVERT: C 191 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: C 249 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7455 (t0) REVERT: C 437 ASP cc_start: 0.7388 (m-30) cc_final: 0.6876 (m-30) REVERT: C 458 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7860 (mtm180) REVERT: C 488 ASP cc_start: 0.7616 (m-30) cc_final: 0.7318 (m-30) REVERT: C 499 LYS cc_start: 0.7680 (tttp) cc_final: 0.7171 (ttpp) REVERT: D 59 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8139 (t0) REVERT: D 101 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7376 (tp30) REVERT: D 107 THR cc_start: 0.8195 (m) cc_final: 0.7848 (t) REVERT: D 191 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7718 (pm20) REVERT: D 249 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7467 (t0) REVERT: D 424 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: D 437 ASP cc_start: 0.7392 (m-30) cc_final: 0.6860 (m-30) REVERT: D 457 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7738 (ttmm) REVERT: D 499 LYS cc_start: 0.7670 (tttp) cc_final: 0.7138 (ttpp) outliers start: 44 outliers final: 19 residues processed: 209 average time/residue: 1.4285 time to fit residues: 330.4909 Evaluate side-chains 212 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 191 GLU 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 392 MET Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 191 GLU 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 12 MET Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 179 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 338 ASN A 226 ASN 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 = 0.3454 r_free = 0.3454 target = 0.129709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109373 restraints weight = 19015.991| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.32 r_work: 0.3096 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16888 Z= 0.234 Angle : 0.580 11.022 23040 Z= 0.288 Chirality : 0.044 0.140 2328 Planarity : 0.004 0.045 3052 Dihedral : 8.169 105.775 2260 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.86 % Allowed : 12.03 % Favored : 85.11 % 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: 0.54 (0.19), residues: 1980 helix: 1.11 (0.20), residues: 684 sheet: 0.53 (0.33), residues: 276 loop : -0.14 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 183 HIS 0.003 0.001 HIS D 218 PHE 0.014 0.002 PHE C 136 TYR 0.017 0.002 TYR D 236 ARG 0.003 0.000 ARG D 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 221 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 1.761 Fit side-chains REVERT: B 59 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8141 (t0) REVERT: B 101 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7378 (tp30) REVERT: B 107 THR cc_start: 0.8228 (m) cc_final: 0.7873 (t) REVERT: B 191 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: B 424 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: B 437 ASP cc_start: 0.7428 (m-30) cc_final: 0.6890 (m-30) REVERT: B 458 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.7857 (mtm180) REVERT: B 488 ASP cc_start: 0.7649 (m-30) cc_final: 0.7326 (m-30) REVERT: B 499 LYS cc_start: 0.7726 (tttp) cc_final: 0.7180 (ttpp) REVERT: A 59 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8115 (t0) REVERT: A 107 THR cc_start: 0.8224 (m) cc_final: 0.7869 (t) REVERT: A 191 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: A 249 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7443 (t0) REVERT: A 424 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6761 (tm-30) REVERT: A 437 ASP cc_start: 0.7399 (m-30) cc_final: 0.6866 (m-30) REVERT: A 458 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7892 (mtm180) REVERT: A 488 ASP cc_start: 0.7654 (m-30) cc_final: 0.7347 (m-30) REVERT: A 499 LYS cc_start: 0.7696 (tttp) cc_final: 0.7175 (ttpp) REVERT: C 12 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8196 (mtm) REVERT: C 101 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7399 (tp30) REVERT: C 107 THR cc_start: 0.8216 (m) cc_final: 0.7858 (t) REVERT: C 191 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: C 249 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7449 (t0) REVERT: C 437 ASP cc_start: 0.7399 (m-30) cc_final: 0.6862 (m-30) REVERT: C 458 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.7867 (mtm180) REVERT: C 488 ASP cc_start: 0.7665 (m-30) cc_final: 0.7357 (m-30) REVERT: C 499 LYS cc_start: 0.7713 (tttp) cc_final: 0.7195 (ttpp) REVERT: D 59 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8130 (t0) REVERT: D 101 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7367 (tp30) REVERT: D 107 THR cc_start: 0.8221 (m) cc_final: 0.7864 (t) REVERT: D 191 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7714 (pm20) REVERT: D 249 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7446 (t0) REVERT: D 424 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6775 (tm-30) REVERT: D 437 ASP cc_start: 0.7402 (m-30) cc_final: 0.6859 (m-30) REVERT: D 488 ASP cc_start: 0.7596 (m-30) cc_final: 0.7357 (m-30) REVERT: D 499 LYS cc_start: 0.7718 (tttp) cc_final: 0.7161 (ttpp) outliers start: 49 outliers final: 22 residues processed: 208 average time/residue: 1.4325 time to fit residues: 330.5193 Evaluate side-chains 208 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ASP 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 191 GLU 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 392 MET Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 191 GLU 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 C residue 12 MET Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 361 THR 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 171 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.0470 chunk 46 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.130977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110809 restraints weight = 19034.556| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.32 r_work: 0.3113 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16888 Z= 0.194 Angle : 0.560 12.084 23040 Z= 0.277 Chirality : 0.044 0.150 2328 Planarity : 0.004 0.044 3052 Dihedral : 7.824 97.461 2260 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.39 % Allowed : 12.32 % Favored : 85.28 % 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: 0.60 (0.19), residues: 1980 helix: 1.21 (0.20), residues: 680 sheet: 0.58 (0.33), residues: 276 loop : -0.14 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 183 HIS 0.005 0.001 HIS C 102 PHE 0.012 0.001 PHE C 136 TYR 0.016 0.001 TYR C 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 219 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 1.869 Fit side-chains REVERT: B 12 MET cc_start: 0.8506 (mtm) cc_final: 0.8123 (mtm) REVERT: B 59 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8043 (t0) REVERT: B 107 THR cc_start: 0.8207 (m) cc_final: 0.7858 (t) REVERT: B 191 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: B 424 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: B 437 ASP cc_start: 0.7416 (m-30) cc_final: 0.6868 (m-30) REVERT: B 458 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.7872 (mtm180) REVERT: B 488 ASP cc_start: 0.7636 (m-30) cc_final: 0.7316 (m-30) REVERT: B 499 LYS cc_start: 0.7706 (tttp) cc_final: 0.7162 (ttpp) REVERT: A 12 MET cc_start: 0.8527 (mtm) cc_final: 0.8190 (mtm) REVERT: A 19 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.6436 (ttm-80) REVERT: A 59 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8031 (t0) REVERT: A 107 THR cc_start: 0.8182 (m) cc_final: 0.7842 (t) REVERT: A 191 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: A 249 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7447 (t0) REVERT: A 424 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: A 437 ASP cc_start: 0.7382 (m-30) cc_final: 0.6814 (m-30) REVERT: A 458 ARG cc_start: 0.8253 (mtp180) cc_final: 0.7901 (mtm180) REVERT: A 488 ASP cc_start: 0.7651 (m-30) cc_final: 0.7367 (m-30) REVERT: A 499 LYS cc_start: 0.7696 (tttp) cc_final: 0.7144 (ttpp) REVERT: C 12 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8195 (mtm) REVERT: C 101 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7396 (tp30) REVERT: C 107 THR cc_start: 0.8190 (m) cc_final: 0.7844 (t) REVERT: C 191 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: C 249 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7438 (t0) REVERT: C 424 GLN cc_start: 0.7710 (tp40) cc_final: 0.7397 (tm-30) REVERT: C 437 ASP cc_start: 0.7387 (m-30) cc_final: 0.7072 (m-30) REVERT: C 458 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7887 (mtm180) REVERT: C 488 ASP cc_start: 0.7677 (m-30) cc_final: 0.7392 (m-30) REVERT: C 499 LYS cc_start: 0.7744 (tttp) cc_final: 0.7185 (ttpp) REVERT: D 59 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8061 (t0) REVERT: D 107 THR cc_start: 0.8191 (m) cc_final: 0.7845 (t) REVERT: D 191 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: D 249 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7474 (t0) REVERT: D 424 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6766 (tm-30) REVERT: D 437 ASP cc_start: 0.7389 (m-30) cc_final: 0.6811 (m-30) REVERT: D 458 ARG cc_start: 0.8381 (ttp-170) cc_final: 0.8120 (mtm180) REVERT: D 488 ASP cc_start: 0.7595 (m-30) cc_final: 0.7371 (m-30) REVERT: D 499 LYS cc_start: 0.7691 (tttp) cc_final: 0.7136 (ttpp) outliers start: 41 outliers final: 20 residues processed: 208 average time/residue: 1.4116 time to fit residues: 324.2310 Evaluate side-chains 207 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 191 GLU 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 C residue 12 MET 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 191 GLU 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 59 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 118 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 86 optimal weight: 0.0870 chunk 109 optimal weight: 10.0000 chunk 113 optimal weight: 0.2980 chunk 177 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- 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 ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112196 restraints weight = 18909.840| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.32 r_work: 0.3138 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16888 Z= 0.171 Angle : 0.536 10.378 23040 Z= 0.267 Chirality : 0.043 0.138 2328 Planarity : 0.004 0.044 3052 Dihedral : 7.479 87.918 2260 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.28 % Allowed : 12.50 % Favored : 85.22 % 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: 0.71 (0.19), residues: 1980 helix: 1.24 (0.20), residues: 684 sheet: 0.44 (0.32), residues: 304 loop : 0.04 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 183 HIS 0.003 0.001 HIS A 235 PHE 0.012 0.001 PHE D 136 TYR 0.015 0.001 TYR A 236 ARG 0.003 0.000 ARG D 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10339.77 seconds wall clock time: 183 minutes 46.20 seconds (11026.20 seconds total)