Starting phenix.real_space_refine on Sun Aug 24 02:43:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wzk_37955/08_2025/8wzk_37955.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wzk_37955/08_2025/8wzk_37955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wzk_37955/08_2025/8wzk_37955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wzk_37955/08_2025/8wzk_37955.map" model { file = "/net/cci-nas-00/data/ceres_data/8wzk_37955/08_2025/8wzk_37955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wzk_37955/08_2025/8wzk_37955.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16368 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: A, C, D Time building chain proxies: 3.10, per 1000 atoms: 0.19 Number of scatterers: 16368 At special positions: 0 Unit cell: (108.07, 114.49, 84.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 12 15.00 O 3024 8.00 N 2884 7.00 C 10392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 591.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3712 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 39.0% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 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: 3.625A 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: 3.895A 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: 3.912A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.563A 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: 3.642A 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: 3.625A 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: 3.895A 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: 3.912A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.563A 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: 3.642A 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: 3.625A 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: 3.895A 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: 3.912A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.562A 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: 3.641A 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: 3.625A 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: 3.895A 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: 3.912A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) removed outlier: 3.563A 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: 3.642A 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 removed outlier: 3.979A pdb=" N ILE A 423 " --> pdb=" O VAL D 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 343 through 345 removed outlier: 5.955A pdb=" N ILE B 281 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 423 through 424 removed outlier: 3.979A pdb=" N ILE B 423 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 423 through 424 removed outlier: 3.979A pdb=" N ILE C 423 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 5.954A pdb=" N ILE A 281 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.977A pdb=" N ILE D 423 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 345 removed outlier: 5.955A pdb=" N ILE C 281 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.160A 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: 5.954A pdb=" N ILE D 281 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 5884 1.37 - 1.56: 10880 1.56 - 1.76: 20 1.76 - 1.95: 92 1.95 - 2.14: 12 Bond restraints: 16888 Sorted by residual: bond pdb=" O2B NDP D3002 " pdb=" P2B NDP D3002 " ideal model delta sigma weight residual 1.833 1.620 0.213 3.80e-02 6.93e+02 3.13e+01 bond pdb=" O2B NDP A3002 " pdb=" P2B NDP A3002 " ideal model delta sigma weight residual 1.833 1.620 0.213 3.80e-02 6.93e+02 3.13e+01 bond pdb=" O2B NDP C3002 " pdb=" P2B NDP C3002 " ideal model delta sigma weight residual 1.833 1.620 0.213 3.80e-02 6.93e+02 3.13e+01 bond pdb=" O2B NDP B3002 " pdb=" P2B NDP B3002 " ideal model delta sigma weight residual 1.833 1.621 0.212 3.80e-02 6.93e+02 3.11e+01 bond pdb=" C VAL D 111 " pdb=" O VAL D 111 " ideal model delta sigma weight residual 1.236 1.283 -0.047 1.02e-02 9.61e+03 2.10e+01 ... (remaining 16883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 22690 4.45 - 8.89: 318 8.89 - 13.34: 20 13.34 - 17.79: 8 17.79 - 22.23: 4 Bond angle restraints: 23040 Sorted by residual: angle pdb=" PA NDP B3002 " pdb=" O3 NDP B3002 " pdb=" PN NDP B3002 " ideal model delta sigma weight residual 107.74 129.97 -22.23 1.95e+00 2.62e-01 1.29e+02 angle pdb=" PA NDP D3002 " pdb=" O3 NDP D3002 " pdb=" PN NDP D3002 " ideal model delta sigma weight residual 107.74 129.97 -22.23 1.95e+00 2.62e-01 1.29e+02 angle pdb=" PA NDP C3002 " pdb=" O3 NDP C3002 " pdb=" PN NDP C3002 " ideal model delta sigma weight residual 107.74 129.96 -22.22 1.95e+00 2.62e-01 1.29e+02 angle pdb=" PA NDP A3002 " pdb=" O3 NDP A3002 " pdb=" PN NDP A3002 " ideal model delta sigma weight residual 107.74 129.96 -22.22 1.95e+00 2.62e-01 1.29e+02 angle pdb=" C5B NDP B3002 " pdb=" O5B NDP B3002 " pdb=" PA NDP B3002 " ideal model delta sigma weight residual 103.84 121.48 -17.64 1.91e+00 2.73e-01 8.48e+01 ... (remaining 23035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.79: 9102 19.79 - 39.59: 589 39.59 - 59.38: 113 59.38 - 79.17: 40 79.17 - 98.96: 16 Dihedral angle restraints: 9860 sinusoidal: 4080 harmonic: 5780 Sorted by residual: 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 180.00 154.53 25.47 0 5.00e+00 4.00e-02 2.59e+01 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 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP B 389 " pdb=" C ASP B 389 " pdb=" N GLY B 390 " pdb=" CA GLY B 390 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 9857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 971 0.048 - 0.096: 759 0.096 - 0.144: 443 0.144 - 0.192: 120 0.192 - 0.241: 35 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA ILE B 311 " pdb=" N ILE B 311 " pdb=" C ILE B 311 " pdb=" CB ILE B 311 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE D 311 " pdb=" N ILE D 311 " pdb=" C ILE D 311 " pdb=" CB ILE D 311 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE A 311 " pdb=" N ILE A 311 " pdb=" C ILE A 311 " pdb=" CB ILE A 311 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2325 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEM D3001 " 0.072 2.00e-02 2.50e+03 4.02e-02 3.63e+01 pdb=" C2C HEM D3001 " 0.049 2.00e-02 2.50e+03 pdb=" C3C HEM D3001 " 0.006 2.00e-02 2.50e+03 pdb=" C4C HEM D3001 " -0.014 2.00e-02 2.50e+03 pdb=" CAC HEM D3001 " -0.040 2.00e-02 2.50e+03 pdb=" CHC HEM D3001 " -0.071 2.00e-02 2.50e+03 pdb=" CHD HEM D3001 " 0.005 2.00e-02 2.50e+03 pdb=" CMC HEM D3001 " -0.004 2.00e-02 2.50e+03 pdb=" NC HEM D3001 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM B3001 " 0.072 2.00e-02 2.50e+03 4.00e-02 3.59e+01 pdb=" C2C HEM B3001 " 0.049 2.00e-02 2.50e+03 pdb=" C3C HEM B3001 " 0.007 2.00e-02 2.50e+03 pdb=" C4C HEM B3001 " -0.014 2.00e-02 2.50e+03 pdb=" CAC HEM B3001 " -0.040 2.00e-02 2.50e+03 pdb=" CHC HEM B3001 " -0.070 2.00e-02 2.50e+03 pdb=" CHD HEM B3001 " 0.005 2.00e-02 2.50e+03 pdb=" CMC HEM B3001 " -0.004 2.00e-02 2.50e+03 pdb=" NC HEM B3001 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM C3001 " -0.072 2.00e-02 2.50e+03 3.99e-02 3.58e+01 pdb=" C2C HEM C3001 " -0.049 2.00e-02 2.50e+03 pdb=" C3C HEM C3001 " -0.006 2.00e-02 2.50e+03 pdb=" C4C HEM C3001 " 0.014 2.00e-02 2.50e+03 pdb=" CAC HEM C3001 " 0.039 2.00e-02 2.50e+03 pdb=" CHC HEM C3001 " 0.070 2.00e-02 2.50e+03 pdb=" CHD HEM C3001 " -0.005 2.00e-02 2.50e+03 pdb=" CMC HEM C3001 " 0.004 2.00e-02 2.50e+03 pdb=" NC HEM C3001 " 0.005 2.00e-02 2.50e+03 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5403 2.88 - 3.39: 15743 3.39 - 3.89: 30676 3.89 - 4.40: 35266 4.40 - 4.90: 57765 Nonbonded interactions: 144853 Sorted by model distance: nonbonded pdb=" O ARG D 388 " pdb=" O ASP D 389 " model vdw 2.379 3.040 nonbonded pdb=" O ARG A 388 " pdb=" O ASP A 389 " model vdw 2.379 3.040 nonbonded pdb=" O ARG B 388 " pdb=" O ASP B 389 " model vdw 2.380 3.040 nonbonded pdb=" O ARG C 388 " pdb=" O ASP C 389 " model vdw 2.380 3.040 nonbonded pdb=" OD1 ASP A 298 " pdb=" OG1 THR A 300 " model vdw 2.389 3.040 ... (remaining 144848 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.180 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 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 : 0.016 0.213 16892 Z= 1.059 Angle : 1.797 22.233 23040 Z= 1.232 Chirality : 0.082 0.241 2328 Planarity : 0.009 0.045 3052 Dihedral : 14.605 98.964 6148 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.84 % Favored : 95.96 % Rotamer: Outliers : 1.87 % Allowed : 4.67 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.17), residues: 1980 helix: -0.51 (0.17), residues: 684 sheet: -0.29 (0.31), residues: 276 loop : -1.06 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.003 ARG C 72 TYR 0.038 0.009 TYR A 236 PHE 0.046 0.009 PHE B 334 TRP 0.034 0.012 TRP C 277 HIS 0.031 0.006 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.01561 (16888) covalent geometry : angle 1.79686 (23040) hydrogen bonds : bond 0.18027 ( 660) hydrogen bonds : angle 8.43268 ( 1884) Misc. bond : bond 0.02100 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 332 time to evaluate : 0.396 Fit side-chains REVERT: B 12 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5776 (mtm) REVERT: B 93 LYS cc_start: 0.6283 (ptmt) cc_final: 0.5971 (mtpt) REVERT: B 94 TYR cc_start: 0.6983 (m-80) cc_final: 0.6775 (m-80) REVERT: B 98 LYS cc_start: 0.6813 (mttt) cc_final: 0.6305 (mtpt) REVERT: B 139 GLU cc_start: 0.5948 (mm-30) cc_final: 0.5400 (mt-10) REVERT: B 140 ASP cc_start: 0.6392 (m-30) cc_final: 0.6190 (m-30) REVERT: B 228 GLU cc_start: 0.5895 (mp0) cc_final: 0.5649 (tt0) REVERT: B 232 CYS cc_start: 0.7278 (t) cc_final: 0.6705 (p) REVERT: B 256 GLU cc_start: 0.6407 (mm-30) cc_final: 0.6185 (mt-10) REVERT: B 273 LYS cc_start: 0.5473 (mtmm) cc_final: 0.5262 (mmtm) REVERT: B 306 LYS cc_start: 0.6350 (mppt) cc_final: 0.6143 (mppt) REVERT: B 389 ASP cc_start: 0.5162 (OUTLIER) cc_final: 0.4598 (m-30) REVERT: B 396 ASP cc_start: 0.5060 (p0) cc_final: 0.4731 (p0) REVERT: B 422 SER cc_start: 0.6995 (p) cc_final: 0.6763 (t) REVERT: B 423 ILE cc_start: 0.6283 (OUTLIER) cc_final: 0.5850 (mp) REVERT: B 428 GLU cc_start: 0.6026 (mp0) cc_final: 0.5818 (mt-10) REVERT: B 453 GLU cc_start: 0.5781 (tp30) cc_final: 0.5378 (tp30) REVERT: B 466 HIS cc_start: 0.7133 (t-90) cc_final: 0.6832 (t-90) REVERT: B 484 GLU cc_start: 0.6868 (tt0) cc_final: 0.6454 (tt0) REVERT: A 12 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5767 (mtm) REVERT: A 93 LYS cc_start: 0.6289 (ptmt) cc_final: 0.5978 (mtpt) REVERT: A 94 TYR cc_start: 0.6984 (m-80) cc_final: 0.6781 (m-80) REVERT: A 98 LYS cc_start: 0.6816 (mttt) cc_final: 0.6313 (mtpt) REVERT: A 139 GLU cc_start: 0.5948 (mm-30) cc_final: 0.5400 (mt-10) REVERT: A 140 ASP cc_start: 0.6395 (m-30) cc_final: 0.6192 (m-30) REVERT: A 228 GLU cc_start: 0.5927 (mp0) cc_final: 0.5683 (tt0) REVERT: A 232 CYS cc_start: 0.7280 (t) cc_final: 0.6703 (p) REVERT: A 256 GLU cc_start: 0.6416 (mm-30) cc_final: 0.6197 (mt-10) REVERT: A 273 LYS cc_start: 0.5475 (mtmm) cc_final: 0.5264 (mmtm) REVERT: A 306 LYS cc_start: 0.6350 (mppt) cc_final: 0.6143 (mppt) REVERT: A 389 ASP cc_start: 0.5158 (OUTLIER) cc_final: 0.4596 (m-30) REVERT: A 396 ASP cc_start: 0.5055 (p0) cc_final: 0.4727 (p0) REVERT: A 422 SER cc_start: 0.6994 (p) cc_final: 0.6755 (t) REVERT: A 423 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5732 (mp) REVERT: A 428 GLU cc_start: 0.6028 (mp0) cc_final: 0.5818 (mt-10) REVERT: A 453 GLU cc_start: 0.5777 (tp30) cc_final: 0.5374 (tp30) REVERT: A 466 HIS cc_start: 0.7134 (t-90) cc_final: 0.6832 (t-90) REVERT: A 484 GLU cc_start: 0.6884 (tt0) cc_final: 0.6468 (tt0) REVERT: C 12 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5763 (mtm) REVERT: C 93 LYS cc_start: 0.6282 (ptmt) cc_final: 0.5971 (mtpt) REVERT: C 94 TYR cc_start: 0.6981 (m-80) cc_final: 0.6776 (m-80) REVERT: C 98 LYS cc_start: 0.6818 (mttt) cc_final: 0.6477 (mttm) REVERT: C 139 GLU cc_start: 0.5950 (mm-30) cc_final: 0.5420 (mt-10) REVERT: C 228 GLU cc_start: 0.5926 (mp0) cc_final: 0.5684 (tt0) REVERT: C 232 CYS cc_start: 0.7279 (t) cc_final: 0.6703 (p) REVERT: C 256 GLU cc_start: 0.6408 (mm-30) cc_final: 0.6187 (mt-10) REVERT: C 273 LYS cc_start: 0.5474 (mtmm) cc_final: 0.5262 (mmtm) REVERT: C 306 LYS cc_start: 0.6351 (mppt) cc_final: 0.6142 (mppt) REVERT: C 389 ASP cc_start: 0.5161 (OUTLIER) cc_final: 0.4598 (m-30) REVERT: C 396 ASP cc_start: 0.5057 (p0) cc_final: 0.4729 (p0) REVERT: C 422 SER cc_start: 0.6998 (p) cc_final: 0.6762 (t) REVERT: C 423 ILE cc_start: 0.6164 (OUTLIER) cc_final: 0.5733 (mp) REVERT: C 428 GLU cc_start: 0.6025 (mp0) cc_final: 0.5801 (mt-10) REVERT: C 453 GLU cc_start: 0.5778 (tp30) cc_final: 0.5376 (tp30) REVERT: C 466 HIS cc_start: 0.7133 (t-90) cc_final: 0.6834 (t-90) REVERT: C 484 GLU cc_start: 0.6867 (tt0) cc_final: 0.6454 (tt0) REVERT: D 12 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5771 (mtm) REVERT: D 93 LYS cc_start: 0.6280 (ptmt) cc_final: 0.5970 (mtpt) REVERT: D 94 TYR cc_start: 0.6980 (m-80) cc_final: 0.6774 (m-80) REVERT: D 98 LYS cc_start: 0.6816 (mttt) cc_final: 0.6475 (mttm) REVERT: D 139 GLU cc_start: 0.5952 (mm-30) cc_final: 0.5423 (mt-10) REVERT: D 228 GLU cc_start: 0.5928 (mp0) cc_final: 0.5685 (tt0) REVERT: D 232 CYS cc_start: 0.7279 (t) cc_final: 0.6704 (p) REVERT: D 256 GLU cc_start: 0.6406 (mm-30) cc_final: 0.6193 (mt-10) REVERT: D 273 LYS cc_start: 0.5475 (mtmm) cc_final: 0.5263 (mmtm) REVERT: D 306 LYS cc_start: 0.6351 (mppt) cc_final: 0.6143 (mppt) REVERT: D 389 ASP cc_start: 0.5163 (OUTLIER) cc_final: 0.4599 (m-30) REVERT: D 396 ASP cc_start: 0.5058 (p0) cc_final: 0.4701 (p0) REVERT: D 422 SER cc_start: 0.6998 (p) cc_final: 0.6761 (t) REVERT: D 423 ILE cc_start: 0.6166 (OUTLIER) cc_final: 0.5734 (mp) REVERT: D 428 GLU cc_start: 0.6027 (mp0) cc_final: 0.5816 (mt-10) REVERT: D 453 GLU cc_start: 0.5778 (tp30) cc_final: 0.5376 (tp30) REVERT: D 466 HIS cc_start: 0.7134 (t-90) cc_final: 0.6833 (t-90) REVERT: D 484 GLU cc_start: 0.6867 (tt0) cc_final: 0.6454 (tt0) outliers start: 32 outliers final: 8 residues processed: 348 average time/residue: 0.5742 time to fit residues: 220.3491 Evaluate side-chains 264 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 244 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 368 PRO Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 368 PRO Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 368 PRO Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 368 PRO Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 423 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.166539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.145857 restraints weight = 16110.565| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.02 r_work: 0.3504 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16892 Z= 0.126 Angle : 0.609 8.488 23040 Z= 0.304 Chirality : 0.045 0.151 2328 Planarity : 0.004 0.042 3052 Dihedral : 9.074 109.682 2300 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.17 % Allowed : 9.29 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.19), residues: 1980 helix: 1.24 (0.20), residues: 688 sheet: 0.67 (0.31), residues: 300 loop : -0.43 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.019 0.001 TYR D 236 PHE 0.013 0.002 PHE C 57 TRP 0.008 0.001 TRP C 15 HIS 0.003 0.001 HIS D 466 Details of bonding type rmsd covalent geometry : bond 0.00293 (16888) covalent geometry : angle 0.60920 (23040) hydrogen bonds : bond 0.04750 ( 660) hydrogen bonds : angle 5.93405 ( 1884) Misc. bond : bond 0.00699 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 273 time to evaluate : 0.402 Fit side-chains REVERT: B 12 MET cc_start: 0.7208 (mtm) cc_final: 0.6773 (mtm) REVERT: B 93 LYS cc_start: 0.6721 (ptmt) cc_final: 0.6441 (mtmt) REVERT: B 98 LYS cc_start: 0.7858 (mttt) cc_final: 0.7540 (mttm) REVERT: B 139 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6229 (mm-30) REVERT: B 180 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: B 389 ASP cc_start: 0.5806 (OUTLIER) cc_final: 0.4968 (m-30) REVERT: B 396 ASP cc_start: 0.6472 (p0) cc_final: 0.5891 (p0) REVERT: B 423 ILE cc_start: 0.7677 (mm) cc_final: 0.7477 (mp) REVERT: B 453 GLU cc_start: 0.6805 (tp30) cc_final: 0.6557 (tp30) REVERT: A 12 MET cc_start: 0.7191 (mtm) cc_final: 0.6753 (mtm) REVERT: A 93 LYS cc_start: 0.6720 (ptmt) cc_final: 0.6381 (mtpt) REVERT: A 98 LYS cc_start: 0.7862 (mttt) cc_final: 0.7545 (mttm) REVERT: A 139 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6226 (mm-30) REVERT: A 180 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: A 389 ASP cc_start: 0.5814 (OUTLIER) cc_final: 0.4977 (m-30) REVERT: A 396 ASP cc_start: 0.6450 (p0) cc_final: 0.5870 (p0) REVERT: A 423 ILE cc_start: 0.7642 (mm) cc_final: 0.7437 (mp) REVERT: A 453 GLU cc_start: 0.6835 (tp30) cc_final: 0.6586 (tp30) REVERT: C 12 MET cc_start: 0.7190 (mtm) cc_final: 0.6744 (mtm) REVERT: C 93 LYS cc_start: 0.6710 (ptmt) cc_final: 0.6374 (mtpt) REVERT: C 98 LYS cc_start: 0.7762 (mttt) cc_final: 0.7178 (mttm) REVERT: C 180 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: C 389 ASP cc_start: 0.5816 (OUTLIER) cc_final: 0.4978 (m-30) REVERT: C 396 ASP cc_start: 0.6473 (p0) cc_final: 0.5895 (p0) REVERT: C 423 ILE cc_start: 0.7687 (mm) cc_final: 0.7470 (mp) REVERT: C 453 GLU cc_start: 0.6830 (tp30) cc_final: 0.6578 (tp30) REVERT: D 12 MET cc_start: 0.7195 (mtm) cc_final: 0.6761 (mtm) REVERT: D 93 LYS cc_start: 0.6709 (ptmt) cc_final: 0.6376 (mtpt) REVERT: D 98 LYS cc_start: 0.7772 (mttt) cc_final: 0.7186 (mttm) REVERT: D 180 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7302 (m-30) REVERT: D 389 ASP cc_start: 0.5811 (OUTLIER) cc_final: 0.4966 (m-30) REVERT: D 396 ASP cc_start: 0.6468 (p0) cc_final: 0.5884 (p0) REVERT: D 423 ILE cc_start: 0.7674 (mm) cc_final: 0.7452 (mp) REVERT: D 453 GLU cc_start: 0.6830 (tp30) cc_final: 0.6579 (tp30) outliers start: 20 outliers final: 8 residues processed: 281 average time/residue: 0.5412 time to fit residues: 168.5169 Evaluate side-chains 233 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ASP 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 128 ASP 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 128 ASP 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 128 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN B 421 HIS ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN A 421 HIS ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN C 421 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN D 421 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.162192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.141800 restraints weight = 16490.962| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.01 r_work: 0.3462 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16892 Z= 0.164 Angle : 0.676 12.224 23040 Z= 0.329 Chirality : 0.046 0.142 2328 Planarity : 0.005 0.046 3052 Dihedral : 9.361 122.858 2268 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.22 % Allowed : 10.34 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.19), residues: 1980 helix: 1.31 (0.21), residues: 684 sheet: 0.68 (0.32), residues: 296 loop : -0.39 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 363 TYR 0.023 0.002 TYR D 236 PHE 0.018 0.002 PHE C 136 TRP 0.011 0.002 TRP C 15 HIS 0.007 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00386 (16888) covalent geometry : angle 0.67582 (23040) hydrogen bonds : bond 0.05247 ( 660) hydrogen bonds : angle 6.07001 ( 1884) Misc. bond : bond 0.01452 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 0.424 Fit side-chains REVERT: B 12 MET cc_start: 0.7295 (mtm) cc_final: 0.6810 (mtm) REVERT: B 93 LYS cc_start: 0.6922 (ptmt) cc_final: 0.6693 (mtpt) REVERT: B 180 ASP cc_start: 0.7685 (m-30) cc_final: 0.7390 (m-30) REVERT: B 423 ILE cc_start: 0.7558 (mm) cc_final: 0.7340 (mp) REVERT: A 12 MET cc_start: 0.7263 (mtm) cc_final: 0.6759 (mtm) REVERT: A 93 LYS cc_start: 0.6889 (ptmt) cc_final: 0.6681 (mtpt) REVERT: A 180 ASP cc_start: 0.7692 (m-30) cc_final: 0.7405 (m-30) REVERT: A 423 ILE cc_start: 0.7519 (mm) cc_final: 0.7305 (mp) REVERT: C 12 MET cc_start: 0.7281 (mtm) cc_final: 0.6810 (mtm) REVERT: C 93 LYS cc_start: 0.6903 (ptmt) cc_final: 0.6687 (mtpt) REVERT: C 180 ASP cc_start: 0.7705 (m-30) cc_final: 0.7406 (m-30) REVERT: C 423 ILE cc_start: 0.7533 (mm) cc_final: 0.7327 (mp) REVERT: D 12 MET cc_start: 0.7300 (mtm) cc_final: 0.6791 (mtm) REVERT: D 93 LYS cc_start: 0.6912 (ptmt) cc_final: 0.6692 (mtpt) REVERT: D 180 ASP cc_start: 0.7687 (m-30) cc_final: 0.7393 (m-30) REVERT: D 423 ILE cc_start: 0.7532 (mm) cc_final: 0.7321 (mp) outliers start: 38 outliers final: 20 residues processed: 256 average time/residue: 0.5026 time to fit residues: 143.9746 Evaluate side-chains 216 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 53 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 53 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.160025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.139653 restraints weight = 16461.151| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.01 r_work: 0.3443 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16892 Z= 0.212 Angle : 0.756 14.758 23040 Z= 0.367 Chirality : 0.048 0.137 2328 Planarity : 0.006 0.049 3052 Dihedral : 10.017 136.185 2268 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.27 % Allowed : 10.51 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.19), residues: 1980 helix: 1.08 (0.21), residues: 684 sheet: 0.84 (0.31), residues: 304 loop : -0.63 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 363 TYR 0.025 0.002 TYR C 236 PHE 0.021 0.003 PHE B 136 TRP 0.009 0.002 TRP A 183 HIS 0.006 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00503 (16888) covalent geometry : angle 0.75592 (23040) hydrogen bonds : bond 0.05758 ( 660) hydrogen bonds : angle 6.20450 ( 1884) Misc. bond : bond 0.01055 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 0.550 Fit side-chains REVERT: B 12 MET cc_start: 0.7271 (mtm) cc_final: 0.6879 (mtm) REVERT: B 180 ASP cc_start: 0.7644 (m-30) cc_final: 0.7348 (m-30) REVERT: B 237 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7989 (mtpm) REVERT: B 273 LYS cc_start: 0.7497 (mtmm) cc_final: 0.7205 (mmtm) REVERT: A 12 MET cc_start: 0.7273 (mtm) cc_final: 0.6885 (mtm) REVERT: A 180 ASP cc_start: 0.7639 (m-30) cc_final: 0.7342 (m-30) REVERT: A 237 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7999 (mtpm) REVERT: A 273 LYS cc_start: 0.7499 (mtmm) cc_final: 0.7208 (mmtm) REVERT: C 12 MET cc_start: 0.7213 (mtm) cc_final: 0.6821 (mtm) REVERT: C 139 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6140 (pt0) REVERT: C 180 ASP cc_start: 0.7641 (m-30) cc_final: 0.7334 (m-30) REVERT: C 237 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7986 (mtpm) REVERT: C 273 LYS cc_start: 0.7491 (mtmm) cc_final: 0.7194 (mmtm) REVERT: D 12 MET cc_start: 0.7270 (mtm) cc_final: 0.6882 (mtm) REVERT: D 180 ASP cc_start: 0.7639 (m-30) cc_final: 0.7331 (m-30) REVERT: D 237 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7981 (mtpm) REVERT: D 273 LYS cc_start: 0.7496 (mtmm) cc_final: 0.7193 (mmtm) outliers start: 56 outliers final: 29 residues processed: 242 average time/residue: 0.5435 time to fit residues: 145.6172 Evaluate side-chains 222 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 149 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 33 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS A 33 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS C 22 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 HIS D 22 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.163419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.143184 restraints weight = 16295.683| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.01 r_work: 0.3483 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16892 Z= 0.128 Angle : 0.615 8.780 23040 Z= 0.305 Chirality : 0.044 0.143 2328 Planarity : 0.005 0.046 3052 Dihedral : 9.331 127.736 2268 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.10 % Allowed : 11.33 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.19), residues: 1980 helix: 1.36 (0.21), residues: 688 sheet: 0.64 (0.32), residues: 296 loop : -0.33 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.019 0.001 TYR B 236 PHE 0.015 0.002 PHE C 136 TRP 0.009 0.001 TRP D 183 HIS 0.005 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00301 (16888) covalent geometry : angle 0.61511 (23040) hydrogen bonds : bond 0.04519 ( 660) hydrogen bonds : angle 5.92288 ( 1884) Misc. bond : bond 0.01564 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: B 12 MET cc_start: 0.7316 (mtm) cc_final: 0.6886 (mtm) REVERT: B 139 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6342 (pt0) REVERT: B 180 ASP cc_start: 0.7657 (m-30) cc_final: 0.7356 (m-30) REVERT: B 255 GLN cc_start: 0.7524 (tm-30) cc_final: 0.7211 (tm-30) REVERT: B 273 LYS cc_start: 0.7532 (mtmm) cc_final: 0.7224 (mmtm) REVERT: A 12 MET cc_start: 0.7313 (mtm) cc_final: 0.6864 (mtm) REVERT: A 139 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6354 (pt0) REVERT: A 180 ASP cc_start: 0.7663 (m-30) cc_final: 0.7361 (m-30) REVERT: A 255 GLN cc_start: 0.7532 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 273 LYS cc_start: 0.7460 (mtmm) cc_final: 0.7193 (mmtm) REVERT: C 12 MET cc_start: 0.7328 (mtm) cc_final: 0.6879 (mtm) REVERT: C 139 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6240 (pt0) REVERT: C 140 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6605 (t0) REVERT: C 180 ASP cc_start: 0.7660 (m-30) cc_final: 0.7358 (m-30) REVERT: C 273 LYS cc_start: 0.7454 (mtmm) cc_final: 0.7173 (mmtm) REVERT: D 12 MET cc_start: 0.7310 (mtm) cc_final: 0.6867 (mtm) REVERT: D 180 ASP cc_start: 0.7664 (m-30) cc_final: 0.7361 (m-30) REVERT: D 255 GLN cc_start: 0.7515 (tm-30) cc_final: 0.7203 (tm-30) REVERT: D 273 LYS cc_start: 0.7485 (mtmm) cc_final: 0.7201 (mmtm) outliers start: 53 outliers final: 36 residues processed: 235 average time/residue: 0.5727 time to fit residues: 148.2255 Evaluate side-chains 228 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 188 optimal weight: 6.9990 chunk 42 optimal weight: 0.0570 chunk 140 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS A 22 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS D 22 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.163186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.142794 restraints weight = 16399.264| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.02 r_work: 0.3479 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16892 Z= 0.138 Angle : 0.627 10.087 23040 Z= 0.308 Chirality : 0.045 0.140 2328 Planarity : 0.005 0.047 3052 Dihedral : 9.299 127.120 2268 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.10 % Allowed : 11.74 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.19), residues: 1980 helix: 1.34 (0.21), residues: 688 sheet: 0.62 (0.32), residues: 296 loop : -0.29 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 19 TYR 0.020 0.002 TYR C 236 PHE 0.016 0.002 PHE A 136 TRP 0.008 0.001 TRP A 183 HIS 0.005 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00327 (16888) covalent geometry : angle 0.62736 (23040) hydrogen bonds : bond 0.04639 ( 660) hydrogen bonds : angle 5.89173 ( 1884) Misc. bond : bond 0.01165 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: B 12 MET cc_start: 0.7328 (mtm) cc_final: 0.6884 (mtm) REVERT: B 139 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6333 (pt0) REVERT: B 180 ASP cc_start: 0.7662 (m-30) cc_final: 0.7363 (m-30) REVERT: B 255 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7259 (tm-30) REVERT: B 273 LYS cc_start: 0.7508 (mtmm) cc_final: 0.7213 (mmtm) REVERT: A 12 MET cc_start: 0.7319 (mtm) cc_final: 0.6893 (mtm) REVERT: A 139 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6342 (pt0) REVERT: A 180 ASP cc_start: 0.7657 (m-30) cc_final: 0.7364 (m-30) REVERT: A 255 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 273 LYS cc_start: 0.7504 (mtmm) cc_final: 0.7223 (mmtm) REVERT: C 12 MET cc_start: 0.7346 (mtm) cc_final: 0.6905 (mtm) REVERT: C 180 ASP cc_start: 0.7655 (m-30) cc_final: 0.7362 (m-30) REVERT: C 255 GLN cc_start: 0.7531 (tm-30) cc_final: 0.7237 (tm-30) REVERT: C 273 LYS cc_start: 0.7504 (mtmm) cc_final: 0.7211 (mmtm) REVERT: D 12 MET cc_start: 0.7334 (mtm) cc_final: 0.6895 (mtm) REVERT: D 180 ASP cc_start: 0.7654 (m-30) cc_final: 0.7356 (m-30) REVERT: D 255 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7247 (tm-30) REVERT: D 273 LYS cc_start: 0.7513 (mtmm) cc_final: 0.7222 (mmtm) outliers start: 53 outliers final: 39 residues processed: 237 average time/residue: 0.5470 time to fit residues: 144.0025 Evaluate side-chains 226 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 169 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 0.0470 chunk 171 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS A 22 GLN A 173 GLN A 466 HIS C 22 GLN C 173 GLN C 466 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.161361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.140988 restraints weight = 16351.221| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.01 r_work: 0.3457 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16892 Z= 0.188 Angle : 0.711 13.947 23040 Z= 0.344 Chirality : 0.047 0.157 2328 Planarity : 0.006 0.047 3052 Dihedral : 9.753 133.171 2268 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.75 % Allowed : 12.32 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.19), residues: 1980 helix: 1.17 (0.21), residues: 688 sheet: 0.52 (0.32), residues: 296 loop : -0.42 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 19 TYR 0.021 0.002 TYR C 236 PHE 0.019 0.002 PHE B 136 TRP 0.009 0.002 TRP A 183 HIS 0.005 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00448 (16888) covalent geometry : angle 0.71091 (23040) hydrogen bonds : bond 0.05347 ( 660) hydrogen bonds : angle 6.07419 ( 1884) Misc. bond : bond 0.01086 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 0.424 Fit side-chains REVERT: B 12 MET cc_start: 0.7434 (mtm) cc_final: 0.6995 (mtm) REVERT: B 139 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6315 (pt0) REVERT: B 180 ASP cc_start: 0.7669 (m-30) cc_final: 0.7384 (m-30) REVERT: B 255 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7218 (tm-30) REVERT: B 273 LYS cc_start: 0.7548 (mtmm) cc_final: 0.7226 (mmtm) REVERT: A 12 MET cc_start: 0.7426 (mtm) cc_final: 0.6988 (mtm) REVERT: A 139 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6308 (pt0) REVERT: A 180 ASP cc_start: 0.7676 (m-30) cc_final: 0.7390 (m-30) REVERT: A 255 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7242 (tm-30) REVERT: A 273 LYS cc_start: 0.7539 (mtmm) cc_final: 0.7223 (mmtm) REVERT: C 12 MET cc_start: 0.7443 (mtm) cc_final: 0.7023 (mtm) REVERT: C 180 ASP cc_start: 0.7609 (m-30) cc_final: 0.7322 (m-30) REVERT: C 255 GLN cc_start: 0.7545 (tm-30) cc_final: 0.7243 (tm-30) REVERT: C 273 LYS cc_start: 0.7538 (mtmm) cc_final: 0.7211 (mmtm) REVERT: D 12 MET cc_start: 0.7423 (mtm) cc_final: 0.6985 (mtm) REVERT: D 180 ASP cc_start: 0.7613 (m-30) cc_final: 0.7329 (m-30) REVERT: D 255 GLN cc_start: 0.7567 (tm-30) cc_final: 0.7269 (tm-30) REVERT: D 273 LYS cc_start: 0.7536 (mtmm) cc_final: 0.7212 (mmtm) outliers start: 47 outliers final: 45 residues processed: 215 average time/residue: 0.5412 time to fit residues: 128.8861 Evaluate side-chains 219 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 145 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS A 466 HIS C 466 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.161810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.141366 restraints weight = 16375.060| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.02 r_work: 0.3462 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16892 Z= 0.170 Angle : 0.687 12.822 23040 Z= 0.333 Chirality : 0.046 0.138 2328 Planarity : 0.005 0.047 3052 Dihedral : 9.709 132.824 2268 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.92 % Allowed : 12.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.19), residues: 1980 helix: 1.18 (0.21), residues: 688 sheet: 0.43 (0.31), residues: 296 loop : -0.40 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 19 TYR 0.020 0.002 TYR D 236 PHE 0.018 0.002 PHE B 136 TRP 0.009 0.001 TRP C 183 HIS 0.006 0.001 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00404 (16888) covalent geometry : angle 0.68692 (23040) hydrogen bonds : bond 0.05152 ( 660) hydrogen bonds : angle 6.04535 ( 1884) Misc. bond : bond 0.01563 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.481 Fit side-chains REVERT: B 12 MET cc_start: 0.7401 (mtm) cc_final: 0.6969 (mtm) REVERT: B 139 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6325 (pt0) REVERT: B 180 ASP cc_start: 0.7665 (m-30) cc_final: 0.7376 (m-30) REVERT: B 255 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7248 (tm-30) REVERT: B 273 LYS cc_start: 0.7536 (mtmm) cc_final: 0.7220 (mmtm) REVERT: A 12 MET cc_start: 0.7431 (mtm) cc_final: 0.6977 (mtm) REVERT: A 139 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6324 (pt0) REVERT: A 180 ASP cc_start: 0.7672 (m-30) cc_final: 0.7382 (m-30) REVERT: A 255 GLN cc_start: 0.7591 (tm-30) cc_final: 0.7273 (tm-30) REVERT: C 12 MET cc_start: 0.7449 (mtm) cc_final: 0.7012 (mtm) REVERT: C 180 ASP cc_start: 0.7668 (m-30) cc_final: 0.7378 (m-30) REVERT: C 255 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7252 (tm-30) REVERT: D 12 MET cc_start: 0.7405 (mtm) cc_final: 0.6978 (mtm) REVERT: D 180 ASP cc_start: 0.7665 (m-30) cc_final: 0.7377 (m-30) REVERT: D 255 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7247 (tm-30) outliers start: 50 outliers final: 44 residues processed: 215 average time/residue: 0.5329 time to fit residues: 127.5056 Evaluate side-chains 219 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 181 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 43 optimal weight: 0.0970 chunk 163 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS A 466 HIS C 22 GLN C 466 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.163661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.143310 restraints weight = 16338.781| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.02 r_work: 0.3485 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16892 Z= 0.134 Angle : 0.626 9.414 23040 Z= 0.308 Chirality : 0.045 0.141 2328 Planarity : 0.005 0.048 3052 Dihedral : 9.298 126.809 2268 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.69 % Allowed : 12.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.19), residues: 1980 helix: 1.34 (0.21), residues: 688 sheet: 0.41 (0.31), residues: 296 loop : -0.27 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.019 0.001 TYR D 236 PHE 0.015 0.002 PHE B 136 TRP 0.008 0.001 TRP D 183 HIS 0.005 0.001 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00316 (16888) covalent geometry : angle 0.62620 (23040) hydrogen bonds : bond 0.04558 ( 660) hydrogen bonds : angle 5.88988 ( 1884) Misc. bond : bond 0.01779 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.578 Fit side-chains REVERT: B 12 MET cc_start: 0.7258 (mtm) cc_final: 0.6854 (mtm) REVERT: B 139 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6345 (pt0) REVERT: B 180 ASP cc_start: 0.7683 (m-30) cc_final: 0.7396 (m-30) REVERT: B 255 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7257 (tm-30) REVERT: B 273 LYS cc_start: 0.7566 (mtmm) cc_final: 0.7231 (mmtm) REVERT: B 290 GLU cc_start: 0.6543 (mm-30) cc_final: 0.6146 (mp0) REVERT: A 12 MET cc_start: 0.7277 (mtm) cc_final: 0.6846 (mtm) REVERT: A 139 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6346 (pt0) REVERT: A 180 ASP cc_start: 0.7687 (m-30) cc_final: 0.7395 (m-30) REVERT: A 255 GLN cc_start: 0.7569 (tm-30) cc_final: 0.7269 (tm-30) REVERT: C 12 MET cc_start: 0.7299 (mtm) cc_final: 0.6886 (mtm) REVERT: C 180 ASP cc_start: 0.7679 (m-30) cc_final: 0.7387 (m-30) REVERT: C 255 GLN cc_start: 0.7563 (tm-30) cc_final: 0.7255 (tm-30) REVERT: C 290 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6134 (mp0) REVERT: D 12 MET cc_start: 0.7266 (mtm) cc_final: 0.6838 (mtm) REVERT: D 180 ASP cc_start: 0.7679 (m-30) cc_final: 0.7394 (m-30) REVERT: D 255 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7256 (tm-30) outliers start: 46 outliers final: 42 residues processed: 222 average time/residue: 0.5333 time to fit residues: 131.8869 Evaluate side-chains 221 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 72 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 128 optimal weight: 0.1980 chunk 149 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN B 466 HIS A 466 HIS C 466 HIS D 173 GLN D 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.161378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.140976 restraints weight = 16403.925| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.02 r_work: 0.3458 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16892 Z= 0.182 Angle : 0.727 14.197 23040 Z= 0.348 Chirality : 0.047 0.138 2328 Planarity : 0.006 0.047 3052 Dihedral : 9.751 132.807 2268 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.57 % Allowed : 13.26 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.19), residues: 1980 helix: 0.94 (0.21), residues: 712 sheet: 0.35 (0.31), residues: 296 loop : -0.44 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 19 TYR 0.021 0.002 TYR D 236 PHE 0.019 0.002 PHE B 136 TRP 0.010 0.002 TRP B 183 HIS 0.007 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00433 (16888) covalent geometry : angle 0.72720 (23040) hydrogen bonds : bond 0.05321 ( 660) hydrogen bonds : angle 6.06049 ( 1884) Misc. bond : bond 0.01293 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.607 Fit side-chains REVERT: B 12 MET cc_start: 0.7427 (mtm) cc_final: 0.6981 (mtm) REVERT: B 139 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6279 (pt0) REVERT: B 180 ASP cc_start: 0.7680 (m-30) cc_final: 0.7401 (m-30) REVERT: B 255 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7253 (tm-30) REVERT: B 273 LYS cc_start: 0.7559 (mtmm) cc_final: 0.7260 (mmtm) REVERT: A 12 MET cc_start: 0.7438 (mtm) cc_final: 0.6992 (mtm) REVERT: A 139 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6279 (pt0) REVERT: A 180 ASP cc_start: 0.7669 (m-30) cc_final: 0.7389 (m-30) REVERT: A 255 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7277 (tm-30) REVERT: C 12 MET cc_start: 0.7445 (mtm) cc_final: 0.7011 (mtm) REVERT: C 180 ASP cc_start: 0.7659 (m-30) cc_final: 0.7381 (m-30) REVERT: C 255 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7278 (tm-30) REVERT: D 12 MET cc_start: 0.7428 (mtm) cc_final: 0.6986 (mtm) REVERT: D 180 ASP cc_start: 0.7651 (m-30) cc_final: 0.7375 (m-30) REVERT: D 255 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7251 (tm-30) outliers start: 44 outliers final: 42 residues processed: 213 average time/residue: 0.5575 time to fit residues: 131.8681 Evaluate side-chains 219 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 118 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS A 466 HIS C 22 GLN C 466 HIS D 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.162425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.141955 restraints weight = 16308.728| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.02 r_work: 0.3469 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16892 Z= 0.170 Angle : 0.704 12.405 23040 Z= 0.338 Chirality : 0.046 0.143 2328 Planarity : 0.005 0.047 3052 Dihedral : 9.652 130.847 2268 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.63 % Allowed : 13.38 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.19), residues: 1980 helix: 0.95 (0.20), residues: 712 sheet: 0.29 (0.31), residues: 296 loop : -0.39 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 363 TYR 0.020 0.002 TYR D 236 PHE 0.018 0.002 PHE A 136 TRP 0.009 0.001 TRP D 183 HIS 0.006 0.001 HIS D 466 Details of bonding type rmsd covalent geometry : bond 0.00406 (16888) covalent geometry : angle 0.70448 (23040) hydrogen bonds : bond 0.05060 ( 660) hydrogen bonds : angle 6.02025 ( 1884) Misc. bond : bond 0.01496 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5218.36 seconds wall clock time: 89 minutes 34.18 seconds (5374.18 seconds total)