Starting phenix.real_space_refine on Sat Jun 14 17:56:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wzk_37955/06_2025/8wzk_37955.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wzk_37955/06_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_37955/06_2025/8wzk_37955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wzk_37955/06_2025/8wzk_37955.map" model { file = "/net/cci-nas-00/data/ceres_data/8wzk_37955/06_2025/8wzk_37955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wzk_37955/06_2025/8wzk_37955.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16368 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, D Time building chain proxies: 8.83, per 1000 atoms: 0.54 Number of scatterers: 16368 At special positions: 0 Unit cell: (108.07, 114.49, 84.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 12 15.00 O 3024 8.00 N 2884 7.00 C 10392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 2.0 seconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3712 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 39.0% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 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: 5.28 Time building geometry restraints manager: 4.59 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 36.730 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.130 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (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 TRP 0.034 0.012 TRP C 277 HIS 0.031 0.006 HIS B 218 PHE 0.046 0.009 PHE B 334 TYR 0.038 0.009 TYR A 236 ARG 0.034 0.003 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.18027 ( 660) hydrogen bonds : angle 8.43268 ( 1884) covalent geometry : bond 0.01561 (16888) covalent geometry : angle 1.79686 (23040) 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 : 2.350 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: 1.3522 time to fit residues: 519.9319 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 : 1.754 ------------------------------------------------------------------------------- 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 165 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 79 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.167861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.147240 restraints weight = 16107.781| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.02 r_work: 0.3518 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16892 Z= 0.115 Angle : 0.584 6.424 23040 Z= 0.295 Chirality : 0.044 0.145 2328 Planarity : 0.004 0.040 3052 Dihedral : 8.863 107.183 2300 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.17 % Allowed : 9.11 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1980 helix: 1.29 (0.20), residues: 688 sheet: 0.66 (0.31), residues: 300 loop : -0.43 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 15 HIS 0.003 0.001 HIS C 466 PHE 0.012 0.002 PHE D 57 TYR 0.019 0.001 TYR D 236 ARG 0.003 0.000 ARG C 363 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 660) hydrogen bonds : angle 5.86531 ( 1884) covalent geometry : bond 0.00267 (16888) covalent geometry : angle 0.58432 (23040) Misc. bond : bond 0.00558 ( 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 295 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 275 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 MET cc_start: 0.7259 (mtm) cc_final: 0.6784 (mtm) REVERT: B 93 LYS cc_start: 0.6706 (ptmt) cc_final: 0.6426 (mtmt) REVERT: B 98 LYS cc_start: 0.7830 (mttt) cc_final: 0.7521 (mttm) REVERT: B 139 GLU cc_start: 0.6467 (mm-30) cc_final: 0.6181 (mm-30) REVERT: B 180 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7284 (m-30) REVERT: B 389 ASP cc_start: 0.5792 (OUTLIER) cc_final: 0.5114 (m-30) REVERT: B 396 ASP cc_start: 0.6403 (p0) cc_final: 0.5868 (p0) REVERT: B 423 ILE cc_start: 0.7649 (mm) cc_final: 0.7438 (mp) REVERT: B 453 GLU cc_start: 0.6788 (tp30) cc_final: 0.6539 (tp30) REVERT: A 12 MET cc_start: 0.7224 (mtm) cc_final: 0.6748 (mtm) REVERT: A 93 LYS cc_start: 0.6706 (ptmt) cc_final: 0.6418 (mtmt) REVERT: A 98 LYS cc_start: 0.7834 (mttt) cc_final: 0.7525 (mttm) REVERT: A 139 GLU cc_start: 0.6473 (mm-30) cc_final: 0.6183 (mm-30) REVERT: A 180 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7278 (m-30) REVERT: A 389 ASP cc_start: 0.5808 (OUTLIER) cc_final: 0.5124 (m-30) REVERT: A 396 ASP cc_start: 0.6387 (p0) cc_final: 0.5854 (p0) REVERT: A 423 ILE cc_start: 0.7652 (mm) cc_final: 0.7439 (mp) REVERT: A 453 GLU cc_start: 0.6812 (tp30) cc_final: 0.6564 (tp30) REVERT: C 12 MET cc_start: 0.7241 (mtm) cc_final: 0.6757 (mtm) REVERT: C 93 LYS cc_start: 0.6702 (ptmt) cc_final: 0.6420 (mtmt) REVERT: C 98 LYS cc_start: 0.7748 (mttt) cc_final: 0.7198 (mtpp) REVERT: C 139 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6179 (mm-30) REVERT: C 180 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: C 389 ASP cc_start: 0.5813 (OUTLIER) cc_final: 0.5133 (m-30) REVERT: C 396 ASP cc_start: 0.6395 (p0) cc_final: 0.5860 (p0) REVERT: C 423 ILE cc_start: 0.7656 (mm) cc_final: 0.7424 (mp) REVERT: C 453 GLU cc_start: 0.6771 (tp30) cc_final: 0.6520 (tp30) REVERT: D 12 MET cc_start: 0.7236 (mtm) cc_final: 0.6762 (mtm) REVERT: D 93 LYS cc_start: 0.6704 (ptmt) cc_final: 0.6423 (mtmt) REVERT: D 98 LYS cc_start: 0.7744 (mttt) cc_final: 0.7191 (mtpt) REVERT: D 139 GLU cc_start: 0.6493 (mm-30) cc_final: 0.6201 (mm-30) REVERT: D 180 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: D 389 ASP cc_start: 0.5808 (OUTLIER) cc_final: 0.5124 (m-30) REVERT: D 396 ASP cc_start: 0.6392 (p0) cc_final: 0.5853 (p0) REVERT: D 423 ILE cc_start: 0.7650 (mm) cc_final: 0.7412 (mp) REVERT: D 453 GLU cc_start: 0.6773 (tp30) cc_final: 0.6524 (tp30) outliers start: 20 outliers final: 8 residues processed: 283 average time/residue: 1.2402 time to fit residues: 390.2095 Evaluate side-chains 240 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 32 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.163114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.142678 restraints weight = 16156.140| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.01 r_work: 0.3471 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16892 Z= 0.157 Angle : 0.660 11.635 23040 Z= 0.322 Chirality : 0.046 0.143 2328 Planarity : 0.005 0.045 3052 Dihedral : 9.107 117.215 2268 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.23 % Favored : 96.57 % Rotamer: Outliers : 1.64 % Allowed : 10.57 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1980 helix: 1.38 (0.21), residues: 688 sheet: 0.65 (0.32), residues: 296 loop : -0.34 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 15 HIS 0.007 0.001 HIS A 218 PHE 0.017 0.002 PHE D 136 TYR 0.023 0.002 TYR B 236 ARG 0.004 0.001 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 660) hydrogen bonds : angle 6.01747 ( 1884) covalent geometry : bond 0.00369 (16888) covalent geometry : angle 0.65978 (23040) Misc. bond : bond 0.01123 ( 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 262 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 MET cc_start: 0.7296 (mtm) cc_final: 0.6800 (mtm) REVERT: B 93 LYS cc_start: 0.6775 (ptmt) cc_final: 0.6555 (mtpt) REVERT: B 98 LYS cc_start: 0.8198 (mttt) cc_final: 0.7524 (mtpp) REVERT: B 139 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6197 (mm-30) REVERT: B 180 ASP cc_start: 0.7683 (m-30) cc_final: 0.7390 (m-30) REVERT: B 423 ILE cc_start: 0.7541 (mm) cc_final: 0.7323 (mp) REVERT: A 12 MET cc_start: 0.7281 (mtm) cc_final: 0.6782 (mtm) REVERT: A 93 LYS cc_start: 0.6894 (ptmt) cc_final: 0.6670 (mtpt) REVERT: A 98 LYS cc_start: 0.8200 (mttt) cc_final: 0.7523 (mtpp) REVERT: A 139 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6204 (mm-30) REVERT: A 180 ASP cc_start: 0.7686 (m-30) cc_final: 0.7399 (m-30) REVERT: A 423 ILE cc_start: 0.7541 (mm) cc_final: 0.7311 (mp) REVERT: C 12 MET cc_start: 0.7256 (mtm) cc_final: 0.6835 (mtm) REVERT: C 93 LYS cc_start: 0.6879 (ptmt) cc_final: 0.6667 (mtpt) REVERT: C 98 LYS cc_start: 0.8078 (mttt) cc_final: 0.7566 (mttt) REVERT: C 139 GLU cc_start: 0.6503 (mm-30) cc_final: 0.6226 (mm-30) REVERT: C 180 ASP cc_start: 0.7685 (m-30) cc_final: 0.7400 (m-30) REVERT: C 423 ILE cc_start: 0.7543 (mm) cc_final: 0.7331 (mp) REVERT: D 12 MET cc_start: 0.7250 (mtm) cc_final: 0.6807 (mtm) REVERT: D 93 LYS cc_start: 0.6886 (ptmt) cc_final: 0.6670 (mtpt) REVERT: D 98 LYS cc_start: 0.8085 (mttt) cc_final: 0.7402 (mttt) REVERT: D 180 ASP cc_start: 0.7681 (m-30) cc_final: 0.7397 (m-30) REVERT: D 423 ILE cc_start: 0.7534 (mm) cc_final: 0.7317 (mp) outliers start: 28 outliers final: 20 residues processed: 258 average time/residue: 1.1790 time to fit residues: 339.1954 Evaluate side-chains 222 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ASP 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 389 ASP Chi-restraints excluded: chain A residue 128 ASP 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 389 ASP Chi-restraints excluded: chain C residue 128 ASP 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 389 ASP Chi-restraints excluded: chain D residue 128 ASP 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 389 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 61 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 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 53 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.164420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.143859 restraints weight = 16253.395| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.04 r_work: 0.3487 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16892 Z= 0.124 Angle : 0.602 8.383 23040 Z= 0.298 Chirality : 0.044 0.143 2328 Planarity : 0.005 0.047 3052 Dihedral : 8.782 116.968 2268 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.75 % Allowed : 11.33 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 1980 helix: 1.38 (0.21), residues: 696 sheet: 0.81 (0.32), residues: 296 loop : -0.21 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 183 HIS 0.005 0.001 HIS C 218 PHE 0.015 0.002 PHE B 136 TYR 0.020 0.001 TYR D 236 ARG 0.004 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.04431 ( 660) hydrogen bonds : angle 5.82444 ( 1884) covalent geometry : bond 0.00293 (16888) covalent geometry : angle 0.60196 (23040) Misc. bond : bond 0.01064 ( 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 258 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 1.747 Fit side-chains revert: symmetry clash REVERT: B 12 MET cc_start: 0.7394 (mtm) cc_final: 0.6915 (mtm) REVERT: B 93 LYS cc_start: 0.6862 (ptmt) cc_final: 0.6639 (mtpt) REVERT: B 180 ASP cc_start: 0.7715 (m-30) cc_final: 0.7426 (m-30) REVERT: B 237 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7933 (mmtt) REVERT: B 273 LYS cc_start: 0.7456 (mtmm) cc_final: 0.7143 (mmtm) REVERT: B 290 GLU cc_start: 0.6213 (mm-30) cc_final: 0.6006 (mp0) REVERT: B 423 ILE cc_start: 0.7740 (mm) cc_final: 0.7520 (mp) REVERT: B 453 GLU cc_start: 0.6948 (tp30) cc_final: 0.6668 (tp30) REVERT: A 12 MET cc_start: 0.7213 (mtm) cc_final: 0.6728 (mtm) REVERT: A 93 LYS cc_start: 0.6869 (ptmt) cc_final: 0.6638 (mtpt) REVERT: A 180 ASP cc_start: 0.7699 (m-30) cc_final: 0.7403 (m-30) REVERT: A 237 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7927 (mmtt) REVERT: A 273 LYS cc_start: 0.7468 (mtmm) cc_final: 0.7151 (mmtm) REVERT: A 396 ASP cc_start: 0.6580 (OUTLIER) cc_final: 0.6021 (p0) REVERT: A 423 ILE cc_start: 0.7776 (mm) cc_final: 0.7548 (mp) REVERT: C 12 MET cc_start: 0.7226 (mtm) cc_final: 0.6727 (mtm) REVERT: C 93 LYS cc_start: 0.6859 (ptmt) cc_final: 0.6644 (mtpt) REVERT: C 98 LYS cc_start: 0.8047 (mttt) cc_final: 0.7339 (mtpp) REVERT: C 139 GLU cc_start: 0.6491 (mm-30) cc_final: 0.6197 (mm-30) REVERT: C 180 ASP cc_start: 0.7703 (m-30) cc_final: 0.7399 (m-30) REVERT: C 237 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7931 (mmtt) REVERT: C 273 LYS cc_start: 0.7465 (mtmm) cc_final: 0.7148 (mmtm) REVERT: C 290 GLU cc_start: 0.6213 (mm-30) cc_final: 0.6012 (mp0) REVERT: C 423 ILE cc_start: 0.7750 (mm) cc_final: 0.7536 (mp) REVERT: D 12 MET cc_start: 0.7226 (mtm) cc_final: 0.6748 (mtm) REVERT: D 93 LYS cc_start: 0.6908 (ptmt) cc_final: 0.6683 (mtpt) REVERT: D 180 ASP cc_start: 0.7708 (m-30) cc_final: 0.7411 (m-30) REVERT: D 237 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7931 (mmtt) REVERT: D 273 LYS cc_start: 0.7469 (mtmm) cc_final: 0.7150 (mmtm) REVERT: D 290 GLU cc_start: 0.6206 (mm-30) cc_final: 0.6001 (mp0) REVERT: D 423 ILE cc_start: 0.7745 (mm) cc_final: 0.7525 (mp) REVERT: D 453 GLU cc_start: 0.6959 (tp30) cc_final: 0.6660 (tp30) outliers start: 47 outliers final: 32 residues processed: 252 average time/residue: 1.2254 time to fit residues: 343.9184 Evaluate side-chains 237 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 228 GLU 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 228 GLU 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 A residue 396 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 150 THR Chi-restraints excluded: chain C residue 228 GLU 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 150 THR Chi-restraints excluded: chain D residue 228 GLU 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 45 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS C 22 GLN C 33 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS ** 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 = 0.3805 r_free = 0.3805 target = 0.164293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.144098 restraints weight = 16457.703| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.02 r_work: 0.3491 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2532 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= 0.127 Angle : 0.602 9.106 23040 Z= 0.296 Chirality : 0.044 0.138 2328 Planarity : 0.005 0.047 3052 Dihedral : 8.721 114.605 2268 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.86 % Allowed : 11.16 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 1980 helix: 1.33 (0.21), residues: 696 sheet: 0.84 (0.33), residues: 296 loop : -0.21 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 183 HIS 0.006 0.001 HIS C 218 PHE 0.015 0.002 PHE B 136 TYR 0.021 0.001 TYR D 236 ARG 0.004 0.000 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 660) hydrogen bonds : angle 5.82001 ( 1884) covalent geometry : bond 0.00299 (16888) covalent geometry : angle 0.60190 (23040) Misc. bond : bond 0.00986 ( 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 245 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 1.948 Fit side-chains revert: symmetry clash REVERT: B 180 ASP cc_start: 0.7680 (m-30) cc_final: 0.7416 (m-30) REVERT: B 237 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7849 (mtpm) REVERT: B 255 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7278 (tm-30) REVERT: B 273 LYS cc_start: 0.7472 (mtmm) cc_final: 0.7164 (mmtm) REVERT: A 180 ASP cc_start: 0.7679 (m-30) cc_final: 0.7406 (m-30) REVERT: A 237 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7908 (mtpm) REVERT: A 255 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7277 (tm-30) REVERT: A 273 LYS cc_start: 0.7474 (mtmm) cc_final: 0.7171 (mmtm) REVERT: C 180 ASP cc_start: 0.7690 (m-30) cc_final: 0.7410 (m-30) REVERT: C 237 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7910 (mtpm) REVERT: C 255 GLN cc_start: 0.7546 (tm-30) cc_final: 0.7282 (tm-30) REVERT: C 273 LYS cc_start: 0.7479 (mtmm) cc_final: 0.7170 (mmtm) REVERT: C 290 GLU cc_start: 0.6304 (mm-30) cc_final: 0.6090 (mp0) REVERT: D 180 ASP cc_start: 0.7685 (m-30) cc_final: 0.7416 (m-30) REVERT: D 237 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7835 (mtpm) REVERT: D 255 GLN cc_start: 0.7539 (tm-30) cc_final: 0.7276 (tm-30) REVERT: D 273 LYS cc_start: 0.7482 (mtmm) cc_final: 0.7177 (mmtm) REVERT: D 423 ILE cc_start: 0.7664 (mm) cc_final: 0.7463 (mt) outliers start: 49 outliers final: 30 residues processed: 235 average time/residue: 1.6718 time to fit residues: 437.3844 Evaluate side-chains 227 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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 120 SER Chi-restraints excluded: chain B residue 128 ASP 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 237 LYS 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 228 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 237 LYS 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 120 SER Chi-restraints excluded: chain C residue 128 ASP 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 237 LYS 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 150 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 237 LYS 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 61 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 421 HIS B 466 HIS A 22 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS A 466 HIS C 22 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.160327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.140508 restraints weight = 16387.126| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 0.98 r_work: 0.3451 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16892 Z= 0.216 Angle : 0.747 15.000 23040 Z= 0.362 Chirality : 0.048 0.152 2328 Planarity : 0.006 0.049 3052 Dihedral : 9.558 122.463 2268 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.10 % Allowed : 12.21 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 1980 helix: 0.93 (0.20), residues: 708 sheet: 0.80 (0.32), residues: 304 loop : -0.54 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 15 HIS 0.005 0.002 HIS B 218 PHE 0.020 0.003 PHE B 136 TYR 0.024 0.002 TYR A 236 ARG 0.008 0.001 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.05707 ( 660) hydrogen bonds : angle 6.17088 ( 1884) covalent geometry : bond 0.00514 (16888) covalent geometry : angle 0.74695 (23040) Misc. bond : bond 0.01222 ( 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 234 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 ASP cc_start: 0.7689 (m-30) cc_final: 0.7394 (m-30) REVERT: B 237 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7994 (mtpm) REVERT: B 255 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7289 (tm-30) REVERT: B 273 LYS cc_start: 0.7458 (mtmm) cc_final: 0.7174 (mmtm) REVERT: A 180 ASP cc_start: 0.7696 (m-30) cc_final: 0.7397 (m-30) REVERT: A 237 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8001 (mtpm) REVERT: A 255 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 273 LYS cc_start: 0.7449 (mtmm) cc_final: 0.7178 (mmtm) REVERT: C 180 ASP cc_start: 0.7685 (m-30) cc_final: 0.7392 (m-30) REVERT: C 237 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8000 (mtpm) REVERT: C 255 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 273 LYS cc_start: 0.7449 (mtmm) cc_final: 0.7175 (mmtm) REVERT: D 180 ASP cc_start: 0.7679 (m-30) cc_final: 0.7384 (m-30) REVERT: D 237 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7995 (mtpm) REVERT: D 255 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7287 (tm-30) REVERT: D 273 LYS cc_start: 0.7453 (mtmm) cc_final: 0.7166 (mmtm) outliers start: 53 outliers final: 37 residues processed: 220 average time/residue: 1.6253 time to fit residues: 394.9966 Evaluate side-chains 221 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 1.762 ------------------------------------------------------------------------------- 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 228 GLU 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 290 GLU 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 120 SER Chi-restraints excluded: chain A residue 128 ASP 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 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 150 THR Chi-restraints excluded: chain C residue 228 GLU 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 22 GLN 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 228 GLU 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 290 GLU 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 8 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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** A 22 GLN A 33 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 HIS D 33 ASN ** 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 = 0.3799 r_free = 0.3799 target = 0.163854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.143546 restraints weight = 16287.222| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.02 r_work: 0.3487 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.003 0.050 16892 Z= 0.132 Angle : 0.622 9.367 23040 Z= 0.305 Chirality : 0.045 0.144 2328 Planarity : 0.005 0.048 3052 Dihedral : 8.812 108.703 2268 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.51 % Allowed : 12.97 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1980 helix: 1.32 (0.21), residues: 688 sheet: 0.64 (0.32), residues: 296 loop : -0.29 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 183 HIS 0.006 0.001 HIS D 218 PHE 0.016 0.002 PHE B 136 TYR 0.019 0.002 TYR A 236 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04562 ( 660) hydrogen bonds : angle 5.90616 ( 1884) covalent geometry : bond 0.00312 (16888) covalent geometry : angle 0.62205 (23040) Misc. bond : bond 0.01410 ( 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 237 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 ASP cc_start: 0.7695 (m-30) cc_final: 0.7373 (m-30) REVERT: B 255 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7276 (tm-30) REVERT: B 273 LYS cc_start: 0.7445 (mtmm) cc_final: 0.7173 (mmtm) REVERT: A 180 ASP cc_start: 0.7626 (m-30) cc_final: 0.7323 (m-30) REVERT: A 255 GLN cc_start: 0.7546 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 273 LYS cc_start: 0.7441 (mtmm) cc_final: 0.7185 (mmtm) REVERT: C 180 ASP cc_start: 0.7710 (m-30) cc_final: 0.7402 (m-30) REVERT: C 255 GLN cc_start: 0.7542 (tm-30) cc_final: 0.7256 (tm-30) REVERT: C 273 LYS cc_start: 0.7447 (mtmm) cc_final: 0.7177 (mmtm) REVERT: D 180 ASP cc_start: 0.7691 (m-30) cc_final: 0.7405 (m-30) REVERT: D 255 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7266 (tm-30) REVERT: D 273 LYS cc_start: 0.7459 (mtmm) cc_final: 0.7183 (mmtm) outliers start: 43 outliers final: 31 residues processed: 229 average time/residue: 1.2673 time to fit residues: 322.7437 Evaluate side-chains 228 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 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 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 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 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 51 LEU 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 236 TYR 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 126 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 chunk 73 optimal weight: 6.9990 chunk 147 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.166600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.146408 restraints weight = 16338.036| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.03 r_work: 0.3516 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16892 Z= 0.105 Angle : 0.564 7.270 23040 Z= 0.281 Chirality : 0.043 0.142 2328 Planarity : 0.005 0.047 3052 Dihedral : 8.237 97.380 2268 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.10 % Allowed : 13.90 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 1980 helix: 1.37 (0.21), residues: 696 sheet: 0.74 (0.32), residues: 296 loop : -0.12 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 183 HIS 0.003 0.001 HIS D 218 PHE 0.014 0.001 PHE A 136 TYR 0.017 0.001 TYR C 236 ARG 0.005 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 660) hydrogen bonds : angle 5.67217 ( 1884) covalent geometry : bond 0.00248 (16888) covalent geometry : angle 0.56389 (23040) Misc. bond : bond 0.01002 ( 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 245 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 ASP cc_start: 0.7578 (m-30) cc_final: 0.7289 (m-30) REVERT: B 255 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7299 (tm-30) REVERT: B 273 LYS cc_start: 0.7352 (mtmm) cc_final: 0.7053 (mmtm) REVERT: B 389 ASP cc_start: 0.5666 (OUTLIER) cc_final: 0.5023 (m-30) REVERT: A 180 ASP cc_start: 0.7572 (m-30) cc_final: 0.7275 (m-30) REVERT: A 255 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7289 (tm-30) REVERT: A 273 LYS cc_start: 0.7396 (mtmm) cc_final: 0.7090 (mmtm) REVERT: A 389 ASP cc_start: 0.5684 (OUTLIER) cc_final: 0.5126 (m-30) REVERT: C 180 ASP cc_start: 0.7584 (m-30) cc_final: 0.7284 (m-30) REVERT: C 255 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7287 (tm-30) REVERT: C 273 LYS cc_start: 0.7382 (mtmm) cc_final: 0.7079 (mmtm) REVERT: C 389 ASP cc_start: 0.5716 (OUTLIER) cc_final: 0.5059 (m-30) REVERT: D 180 ASP cc_start: 0.7565 (m-30) cc_final: 0.7276 (m-30) REVERT: D 255 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7297 (tm-30) REVERT: D 273 LYS cc_start: 0.7394 (mtmm) cc_final: 0.7083 (mmtm) REVERT: D 389 ASP cc_start: 0.5711 (OUTLIER) cc_final: 0.5051 (m-30) outliers start: 36 outliers final: 23 residues processed: 232 average time/residue: 1.7335 time to fit residues: 451.0848 Evaluate side-chains 217 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU 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 238 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 389 ASP 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 238 THR Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 389 ASP 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 238 THR 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 128 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 290 GLU 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 179 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 B 466 HIS A 173 GLN A 466 HIS C 173 GLN C 466 HIS D 22 GLN D 173 GLN D 466 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.159042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.138964 restraints weight = 16417.821| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 0.99 r_work: 0.3434 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 16892 Z= 0.279 Angle : 0.852 17.972 23040 Z= 0.410 Chirality : 0.052 0.146 2328 Planarity : 0.007 0.051 3052 Dihedral : 9.515 98.073 2268 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.28 % Allowed : 14.25 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1980 helix: 0.94 (0.20), residues: 684 sheet: 0.58 (0.31), residues: 304 loop : -0.66 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 15 HIS 0.009 0.002 HIS B 466 PHE 0.024 0.003 PHE A 136 TYR 0.024 0.003 TYR C 236 ARG 0.007 0.001 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.06372 ( 660) hydrogen bonds : angle 6.32282 ( 1884) covalent geometry : bond 0.00667 (16888) covalent geometry : angle 0.85164 (23040) Misc. bond : bond 0.01544 ( 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 226 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 ASP cc_start: 0.7662 (m-30) cc_final: 0.7389 (m-30) REVERT: B 255 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7367 (tm-30) REVERT: A 180 ASP cc_start: 0.7655 (m-30) cc_final: 0.7371 (m-30) REVERT: A 255 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7370 (tm-30) REVERT: C 180 ASP cc_start: 0.7660 (m-30) cc_final: 0.7364 (m-30) REVERT: C 255 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7361 (tm-30) REVERT: D 180 ASP cc_start: 0.7645 (m-30) cc_final: 0.7347 (m-30) REVERT: D 255 GLN cc_start: 0.7652 (tm-30) cc_final: 0.7360 (tm-30) outliers start: 39 outliers final: 38 residues processed: 220 average time/residue: 1.3806 time to fit residues: 336.6778 Evaluate side-chains 223 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 120 SER Chi-restraints excluded: chain B residue 128 ASP 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 290 GLU 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 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 120 SER Chi-restraints excluded: chain C residue 128 ASP 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 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 290 GLU 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 171 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 172 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 178 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 466 HIS D 421 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 = 0.3804 r_free = 0.3804 target = 0.164243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.143768 restraints weight = 16337.707| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.03 r_work: 0.3490 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16892 Z= 0.127 Angle : 0.628 10.606 23040 Z= 0.308 Chirality : 0.044 0.150 2328 Planarity : 0.005 0.048 3052 Dihedral : 8.534 87.508 2268 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.87 % Allowed : 14.66 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 1980 helix: 1.27 (0.21), residues: 688 sheet: 0.54 (0.32), residues: 296 loop : -0.30 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 183 HIS 0.005 0.001 HIS D 466 PHE 0.015 0.001 PHE B 136 TYR 0.018 0.001 TYR D 236 ARG 0.004 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 660) hydrogen bonds : angle 5.91605 ( 1884) covalent geometry : bond 0.00300 (16888) covalent geometry : angle 0.62754 (23040) Misc. bond : bond 0.02132 ( 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 221 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 ASP cc_start: 0.7631 (m-30) cc_final: 0.7332 (m-30) REVERT: B 255 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7280 (tm-30) REVERT: B 273 LYS cc_start: 0.7462 (mtmm) cc_final: 0.7106 (mmtm) REVERT: B 389 ASP cc_start: 0.5854 (OUTLIER) cc_final: 0.5327 (m-30) REVERT: A 180 ASP cc_start: 0.7636 (m-30) cc_final: 0.7342 (m-30) REVERT: A 255 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 273 LYS cc_start: 0.7374 (mtmm) cc_final: 0.7116 (mmtm) REVERT: A 290 GLU cc_start: 0.6579 (mm-30) cc_final: 0.6183 (mp0) REVERT: A 389 ASP cc_start: 0.5862 (OUTLIER) cc_final: 0.5329 (m-30) REVERT: C 180 ASP cc_start: 0.7635 (m-30) cc_final: 0.7340 (m-30) REVERT: C 255 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7260 (tm-30) REVERT: C 273 LYS cc_start: 0.7365 (mtmm) cc_final: 0.7090 (mmtm) REVERT: C 389 ASP cc_start: 0.5823 (OUTLIER) cc_final: 0.5262 (m-30) REVERT: D 180 ASP cc_start: 0.7624 (m-30) cc_final: 0.7323 (m-30) REVERT: D 255 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7275 (tm-30) REVERT: D 273 LYS cc_start: 0.7369 (mtmm) cc_final: 0.7095 (mmtm) REVERT: D 389 ASP cc_start: 0.5825 (OUTLIER) cc_final: 0.5264 (m-30) outliers start: 32 outliers final: 28 residues processed: 215 average time/residue: 1.3596 time to fit residues: 324.2012 Evaluate side-chains 213 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 128 ASP 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 290 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 128 ASP 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 128 ASP 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 128 ASP 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 290 GLU 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: 6.9990 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 86 optimal weight: 0.0870 chunk 109 optimal weight: 9.9990 chunk 113 optimal weight: 0.4980 chunk 177 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 466 HIS A 466 HIS 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 = 0.3821 r_free = 0.3821 target = 0.165772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.145530 restraints weight = 16251.249| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.03 r_work: 0.3511 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16892 Z= 0.117 Angle : 0.624 13.350 23040 Z= 0.302 Chirality : 0.044 0.142 2328 Planarity : 0.005 0.048 3052 Dihedral : 8.095 76.271 2268 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.87 % Allowed : 14.37 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 1980 helix: 1.33 (0.20), residues: 692 sheet: 0.61 (0.32), residues: 296 loop : -0.14 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 183 HIS 0.005 0.001 HIS C 466 PHE 0.014 0.001 PHE B 136 TYR 0.018 0.001 TYR B 236 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 660) hydrogen bonds : angle 5.81453 ( 1884) covalent geometry : bond 0.00276 (16888) covalent geometry : angle 0.62406 (23040) Misc. bond : bond 0.02019 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12764.83 seconds wall clock time: 222 minutes 30.91 seconds (13350.91 seconds total)