Starting phenix.real_space_refine on Sun May 18 07:24:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvd_17962/05_2025/8pvd_17962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvd_17962/05_2025/8pvd_17962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pvd_17962/05_2025/8pvd_17962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvd_17962/05_2025/8pvd_17962.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvd_17962/05_2025/8pvd_17962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvd_17962/05_2025/8pvd_17962.cif" } resolution = 3.4 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= 0.001 sd= 0.007 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 10480 2.51 5 N 2908 2.21 5 O 3056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16512 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} 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: 9.32, per 1000 atoms: 0.56 Number of scatterers: 16512 At special positions: 0 Unit cell: (108.141, 109.792, 83.3755, 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 3056 8.00 N 2908 7.00 C 10480 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: 3.92 Conformation dependent library (CDL) restraints added in 1.9 seconds 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3752 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 41.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.592A pdb=" N ARG A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.826A pdb=" N HIS A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 212 " --> pdb=" O HIS A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.792A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Proline residue: A 359 - end of helix removed outlier: 3.563A pdb=" N HIS A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 377 Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 415 through 419 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 504 Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 54 through 66 removed outlier: 3.592A pdb=" N ARG B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.826A pdb=" N HIS B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET B 212 " --> pdb=" O HIS B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 246 through 257 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 366 removed outlier: 3.792A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix removed outlier: 3.563A pdb=" N HIS B 364 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 377 Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 415 through 419 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 504 Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.592A pdb=" N ARG C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.826A pdb=" N HIS C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET C 212 " --> pdb=" O HIS C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 212' Processing helix chain 'C' and resid 246 through 257 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 348 through 366 removed outlier: 3.792A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Proline residue: C 359 - end of helix removed outlier: 3.563A pdb=" N HIS C 364 " --> pdb=" O ASP C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 377 Proline residue: C 374 - end of helix Processing helix chain 'C' and resid 415 through 419 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 504 Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 54 through 66 removed outlier: 3.592A pdb=" N ARG D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 208 through 212 removed outlier: 3.826A pdb=" N HIS D 211 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET D 212 " --> pdb=" O HIS D 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 212' Processing helix chain 'D' and resid 246 through 257 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 348 through 366 removed outlier: 3.792A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) Proline residue: D 359 - end of helix removed outlier: 3.563A pdb=" N HIS D 364 " --> pdb=" O ASP D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 Proline residue: D 374 - end of helix Processing helix chain 'D' and resid 415 through 419 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 504 Processing sheet with id=1, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.452A pdb=" N TRP A 277 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS A 315 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE A 279 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 343 through 345 removed outlier: 6.452A pdb=" N TRP B 277 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS B 315 " --> pdb=" O TRP B 277 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE B 279 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 343 through 345 removed outlier: 6.452A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'D' and resid 343 through 345 removed outlier: 6.452A pdb=" N TRP D 277 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS D 315 " --> pdb=" O TRP D 277 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE D 279 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1860 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 7116 1.39 - 1.57: 9796 1.57 - 1.76: 20 1.76 - 1.94: 92 1.94 - 2.12: 12 Bond restraints: 17036 Sorted by residual: bond pdb=" O2B NDP D 601 " pdb=" P2B NDP D 601 " ideal model delta sigma weight residual 1.833 1.636 0.197 3.80e-02 6.93e+02 2.68e+01 bond pdb=" O2B NDP A 601 " pdb=" P2B NDP A 601 " ideal model delta sigma weight residual 1.833 1.636 0.197 3.80e-02 6.93e+02 2.68e+01 bond pdb=" O2B NDP C 601 " pdb=" P2B NDP C 601 " ideal model delta sigma weight residual 1.833 1.636 0.197 3.80e-02 6.93e+02 2.68e+01 bond pdb=" O2B NDP B 601 " pdb=" P2B NDP B 601 " ideal model delta sigma weight residual 1.833 1.636 0.197 3.80e-02 6.93e+02 2.68e+01 bond pdb=" O5D NDP B 601 " pdb=" PN NDP B 601 " ideal model delta sigma weight residual 1.757 1.594 0.163 3.50e-02 8.16e+02 2.17e+01 ... (remaining 17031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.83: 22832 4.83 - 9.67: 384 9.67 - 14.50: 12 14.50 - 19.34: 8 19.34 - 24.17: 4 Bond angle restraints: 23240 Sorted by residual: angle pdb=" PA NDP A 601 " pdb=" O3 NDP A 601 " pdb=" PN NDP A 601 " ideal model delta sigma weight residual 107.74 131.91 -24.17 1.95e+00 2.62e-01 1.53e+02 angle pdb=" PA NDP B 601 " pdb=" O3 NDP B 601 " pdb=" PN NDP B 601 " ideal model delta sigma weight residual 107.74 131.91 -24.17 1.95e+00 2.62e-01 1.53e+02 angle pdb=" PA NDP D 601 " pdb=" O3 NDP D 601 " pdb=" PN NDP D 601 " ideal model delta sigma weight residual 107.74 131.91 -24.17 1.95e+00 2.62e-01 1.53e+02 angle pdb=" PA NDP C 601 " pdb=" O3 NDP C 601 " pdb=" PN NDP C 601 " ideal model delta sigma weight residual 107.74 131.91 -24.17 1.95e+00 2.62e-01 1.53e+02 angle pdb=" C5B NDP D 601 " pdb=" O5B NDP D 601 " pdb=" PA NDP D 601 " ideal model delta sigma weight residual 103.84 119.74 -15.90 1.91e+00 2.73e-01 6.90e+01 ... (remaining 23235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.52: 9244 19.52 - 39.05: 532 39.05 - 58.57: 112 58.57 - 78.09: 60 78.09 - 97.61: 16 Dihedral angle restraints: 9964 sinusoidal: 4124 harmonic: 5840 Sorted by residual: dihedral pdb=" CA HIS A 218 " pdb=" C HIS A 218 " pdb=" N THR A 219 " pdb=" CA THR A 219 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA HIS B 218 " pdb=" C HIS B 218 " pdb=" N THR B 219 " pdb=" CA THR B 219 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA HIS D 218 " pdb=" C HIS D 218 " pdb=" N THR D 219 " pdb=" CA THR D 219 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 9961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1278 0.061 - 0.121: 664 0.121 - 0.182: 330 0.182 - 0.243: 72 0.243 - 0.303: 4 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA TYR A 236 " pdb=" N TYR A 236 " pdb=" C TYR A 236 " pdb=" CB TYR A 236 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA TYR C 236 " pdb=" N TYR C 236 " pdb=" C TYR C 236 " pdb=" CB TYR C 236 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA TYR B 236 " pdb=" N TYR B 236 " pdb=" C TYR B 236 " pdb=" CB TYR B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 2345 not shown) Planarity restraints: 3080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP D 601 " -0.100 2.00e-02 2.50e+03 6.06e-02 4.59e+01 pdb=" C3N NDP D 601 " -0.005 2.00e-02 2.50e+03 pdb=" C4N NDP D 601 " -0.018 2.00e-02 2.50e+03 pdb=" C7N NDP D 601 " 0.048 2.00e-02 2.50e+03 pdb=" N1N NDP D 601 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP C 601 " -0.100 2.00e-02 2.50e+03 6.06e-02 4.59e+01 pdb=" C3N NDP C 601 " -0.005 2.00e-02 2.50e+03 pdb=" C4N NDP C 601 " -0.018 2.00e-02 2.50e+03 pdb=" C7N NDP C 601 " 0.048 2.00e-02 2.50e+03 pdb=" N1N NDP C 601 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 601 " 0.100 2.00e-02 2.50e+03 6.06e-02 4.59e+01 pdb=" C3N NDP A 601 " 0.005 2.00e-02 2.50e+03 pdb=" C4N NDP A 601 " 0.018 2.00e-02 2.50e+03 pdb=" C7N NDP A 601 " -0.048 2.00e-02 2.50e+03 pdb=" N1N NDP A 601 " -0.075 2.00e-02 2.50e+03 ... (remaining 3077 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 6936 2.96 - 3.44: 16786 3.44 - 3.93: 31468 3.93 - 4.41: 35500 4.41 - 4.90: 56146 Nonbonded interactions: 146836 Sorted by model distance: nonbonded pdb=" OH TYR B 386 " pdb=" O PRO B 412 " model vdw 2.473 3.040 nonbonded pdb=" OH TYR D 386 " pdb=" O PRO D 412 " model vdw 2.473 3.040 nonbonded pdb=" OH TYR C 386 " pdb=" O PRO C 412 " model vdw 2.473 3.040 nonbonded pdb=" OH TYR A 386 " pdb=" O PRO A 412 " model vdw 2.473 3.040 nonbonded pdb=" O PHE D 164 " pdb=" OG SER D 167 " model vdw 2.484 3.040 ... (remaining 146831 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 36.270 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.012 0.197 17040 Z= 0.671 Angle : 1.852 24.172 23240 Z= 1.197 Chirality : 0.086 0.303 2348 Planarity : 0.012 0.116 3080 Dihedral : 15.253 97.608 6212 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.80 % Favored : 96.00 % Rotamer: Outliers : 1.39 % Allowed : 4.40 % Favored : 94.21 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.17), residues: 2000 helix: -0.84 (0.16), residues: 712 sheet: 0.24 (0.30), residues: 276 loop : -0.88 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.007 TRP B 277 HIS 0.018 0.004 HIS D 63 PHE 0.048 0.009 PHE B 334 TYR 0.052 0.009 TYR B 137 ARG 0.038 0.006 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.20555 ( 672) hydrogen bonds : angle 8.46253 ( 1860) covalent geometry : bond 0.01198 (17036) covalent geometry : angle 1.85213 (23240) Misc. bond : bond 0.02093 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 324 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8342 (ptt) cc_final: 0.8036 (ptt) REVERT: A 240 GLN cc_start: 0.6953 (mp-120) cc_final: 0.6386 (mp10) REVERT: A 259 ASP cc_start: 0.6082 (m-30) cc_final: 0.5667 (m-30) REVERT: A 424 GLN cc_start: 0.7233 (tt0) cc_final: 0.6335 (mp10) REVERT: A 428 GLU cc_start: 0.7148 (mt-10) cc_final: 0.5904 (pm20) REVERT: A 430 ARG cc_start: 0.5540 (ptt90) cc_final: 0.5024 (ptt-90) REVERT: A 454 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6707 (mp0) REVERT: A 457 LYS cc_start: 0.5836 (tttm) cc_final: 0.5464 (mptt) REVERT: A 461 GLU cc_start: 0.6143 (mt-10) cc_final: 0.5917 (mt-10) REVERT: B 212 MET cc_start: 0.8348 (ptt) cc_final: 0.8044 (ptt) REVERT: B 240 GLN cc_start: 0.6944 (mp-120) cc_final: 0.6381 (mp10) REVERT: B 259 ASP cc_start: 0.6077 (m-30) cc_final: 0.5667 (m-30) REVERT: B 424 GLN cc_start: 0.7233 (tt0) cc_final: 0.6335 (mp10) REVERT: B 428 GLU cc_start: 0.7148 (mt-10) cc_final: 0.5901 (pm20) REVERT: B 430 ARG cc_start: 0.5541 (ptt90) cc_final: 0.5015 (ptt-90) REVERT: B 454 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6707 (mp0) REVERT: B 457 LYS cc_start: 0.5839 (tttm) cc_final: 0.5464 (mptt) REVERT: B 461 GLU cc_start: 0.6142 (mt-10) cc_final: 0.5918 (mt-10) REVERT: C 212 MET cc_start: 0.8346 (ptt) cc_final: 0.8042 (ptt) REVERT: C 240 GLN cc_start: 0.6946 (mp-120) cc_final: 0.6378 (mp10) REVERT: C 259 ASP cc_start: 0.6082 (m-30) cc_final: 0.5861 (m-30) REVERT: C 424 GLN cc_start: 0.7234 (tt0) cc_final: 0.6330 (mp10) REVERT: C 428 GLU cc_start: 0.7145 (mt-10) cc_final: 0.5940 (pm20) REVERT: C 430 ARG cc_start: 0.5539 (ptt90) cc_final: 0.5020 (ptt-90) REVERT: C 454 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6706 (mp0) REVERT: C 457 LYS cc_start: 0.5838 (tttm) cc_final: 0.5462 (mptt) REVERT: C 461 GLU cc_start: 0.6142 (mt-10) cc_final: 0.5915 (mt-10) REVERT: D 212 MET cc_start: 0.8347 (ptt) cc_final: 0.8042 (ptt) REVERT: D 240 GLN cc_start: 0.6946 (mp-120) cc_final: 0.6382 (mp10) REVERT: D 259 ASP cc_start: 0.6080 (m-30) cc_final: 0.5859 (m-30) REVERT: D 424 GLN cc_start: 0.7233 (tt0) cc_final: 0.6328 (mp10) REVERT: D 428 GLU cc_start: 0.7149 (mt-10) cc_final: 0.5942 (pm20) REVERT: D 430 ARG cc_start: 0.5530 (ptt90) cc_final: 0.5018 (ptt-90) REVERT: D 454 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6703 (mp0) REVERT: D 457 LYS cc_start: 0.5841 (tttm) cc_final: 0.5465 (mptt) REVERT: D 461 GLU cc_start: 0.6145 (mt-10) cc_final: 0.5920 (mt-10) outliers start: 24 outliers final: 0 residues processed: 340 average time/residue: 0.3474 time to fit residues: 166.9590 Evaluate side-chains 162 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 181 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 GLN ** D 407 ASN ** 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 = 0.3235 r_free = 0.3235 target = 0.116474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.101341 restraints weight = 20642.107| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.01 r_work: 0.2916 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17040 Z= 0.119 Angle : 0.584 5.485 23240 Z= 0.300 Chirality : 0.044 0.156 2348 Planarity : 0.004 0.033 3080 Dihedral : 7.756 79.872 2272 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.20 % Favored : 97.60 % Rotamer: Outliers : 1.50 % Allowed : 8.68 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2000 helix: 1.15 (0.19), residues: 712 sheet: 0.49 (0.27), residues: 332 loop : -0.09 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 183 HIS 0.005 0.001 HIS D 235 PHE 0.009 0.001 PHE A 154 TYR 0.021 0.001 TYR B 236 ARG 0.004 0.001 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 672) hydrogen bonds : angle 5.78723 ( 1860) covalent geometry : bond 0.00278 (17036) covalent geometry : angle 0.58389 (23240) Misc. bond : bond 0.00175 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8675 (ptt) cc_final: 0.8466 (ptt) REVERT: A 293 PRO cc_start: 0.8429 (Cg_exo) cc_final: 0.8181 (Cg_endo) REVERT: A 350 MET cc_start: 0.8503 (mmm) cc_final: 0.8268 (mmm) REVERT: A 428 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7149 (mp0) REVERT: A 453 GLU cc_start: 0.5587 (mm-30) cc_final: 0.5384 (mm-30) REVERT: A 457 LYS cc_start: 0.7315 (tttm) cc_final: 0.7082 (mptt) REVERT: B 212 MET cc_start: 0.8676 (ptt) cc_final: 0.8472 (ptt) REVERT: B 293 PRO cc_start: 0.8433 (Cg_exo) cc_final: 0.8184 (Cg_endo) REVERT: B 350 MET cc_start: 0.8537 (mmm) cc_final: 0.8298 (mmm) REVERT: B 428 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7133 (mp0) REVERT: B 453 GLU cc_start: 0.5588 (mm-30) cc_final: 0.5373 (mm-30) REVERT: B 457 LYS cc_start: 0.7301 (tttm) cc_final: 0.7042 (mptt) REVERT: C 212 MET cc_start: 0.8689 (ptt) cc_final: 0.8486 (ptt) REVERT: C 293 PRO cc_start: 0.8423 (Cg_exo) cc_final: 0.8172 (Cg_endo) REVERT: C 350 MET cc_start: 0.8512 (mmm) cc_final: 0.8259 (mmm) REVERT: C 424 GLN cc_start: 0.7222 (tt0) cc_final: 0.6648 (mp10) REVERT: C 453 GLU cc_start: 0.5593 (mm-30) cc_final: 0.5377 (mm-30) REVERT: C 457 LYS cc_start: 0.7319 (tttm) cc_final: 0.7069 (mptt) REVERT: D 212 MET cc_start: 0.8690 (ptt) cc_final: 0.8475 (ptt) REVERT: D 293 PRO cc_start: 0.8432 (Cg_exo) cc_final: 0.8183 (Cg_endo) REVERT: D 350 MET cc_start: 0.8526 (mmm) cc_final: 0.8280 (mmm) REVERT: D 424 GLN cc_start: 0.7272 (tt0) cc_final: 0.6687 (mp10) REVERT: D 453 GLU cc_start: 0.5582 (mm-30) cc_final: 0.5369 (mm-30) REVERT: D 457 LYS cc_start: 0.7303 (tttm) cc_final: 0.7056 (mptt) outliers start: 26 outliers final: 18 residues processed: 194 average time/residue: 0.2755 time to fit residues: 82.4016 Evaluate side-chains 168 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 125 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS C 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.111820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.097309 restraints weight = 21100.074| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 0.99 r_work: 0.2879 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17040 Z= 0.209 Angle : 0.642 7.057 23240 Z= 0.319 Chirality : 0.047 0.151 2348 Planarity : 0.005 0.043 3080 Dihedral : 7.471 78.841 2272 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.62 % Allowed : 9.03 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.51 (0.18), residues: 2000 helix: 1.21 (0.19), residues: 700 sheet: 0.75 (0.30), residues: 284 loop : -0.36 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 183 HIS 0.004 0.001 HIS C 235 PHE 0.015 0.002 PHE C 294 TYR 0.021 0.002 TYR B 236 ARG 0.004 0.001 ARG D 354 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 672) hydrogen bonds : angle 5.77193 ( 1860) covalent geometry : bond 0.00526 (17036) covalent geometry : angle 0.64247 (23240) Misc. bond : bond 0.03878 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.806 Fit side-chains REVERT: A 212 MET cc_start: 0.8915 (ptt) cc_final: 0.8680 (ptt) REVERT: A 240 GLN cc_start: 0.8333 (mp-120) cc_final: 0.7874 (mp10) REVERT: B 212 MET cc_start: 0.8909 (ptt) cc_final: 0.8675 (ptt) REVERT: B 240 GLN cc_start: 0.8332 (mp-120) cc_final: 0.7873 (mp10) REVERT: C 212 MET cc_start: 0.8936 (ptt) cc_final: 0.8707 (ptt) REVERT: C 240 GLN cc_start: 0.8349 (mp-120) cc_final: 0.7883 (mp10) REVERT: D 212 MET cc_start: 0.8910 (ptt) cc_final: 0.8668 (ptt) REVERT: D 240 GLN cc_start: 0.8332 (mp-120) cc_final: 0.7875 (mp10) outliers start: 28 outliers final: 22 residues processed: 160 average time/residue: 0.2587 time to fit residues: 65.1772 Evaluate side-chains 151 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 HIS D 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.111384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.098139 restraints weight = 21514.445| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 0.92 r_work: 0.2905 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17040 Z= 0.178 Angle : 0.597 6.094 23240 Z= 0.295 Chirality : 0.045 0.153 2348 Planarity : 0.005 0.054 3080 Dihedral : 7.299 76.129 2272 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.08 % Allowed : 9.03 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.43 (0.18), residues: 2000 helix: 1.18 (0.19), residues: 708 sheet: 0.57 (0.30), residues: 288 loop : -0.40 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 183 HIS 0.003 0.001 HIS C 235 PHE 0.012 0.002 PHE C 136 TYR 0.020 0.002 TYR A 236 ARG 0.003 0.000 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 672) hydrogen bonds : angle 5.63039 ( 1860) covalent geometry : bond 0.00448 (17036) covalent geometry : angle 0.59700 (23240) Misc. bond : bond 0.02268 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 2.041 Fit side-chains REVERT: A 212 MET cc_start: 0.8963 (ptt) cc_final: 0.8747 (ptt) REVERT: A 240 GLN cc_start: 0.8287 (mp-120) cc_final: 0.7739 (mp10) REVERT: B 212 MET cc_start: 0.8967 (ptt) cc_final: 0.8757 (ptt) REVERT: B 240 GLN cc_start: 0.8270 (mp-120) cc_final: 0.7733 (mp10) REVERT: C 240 GLN cc_start: 0.8290 (mp-120) cc_final: 0.7730 (mp10) REVERT: D 212 MET cc_start: 0.8969 (ptt) cc_final: 0.8755 (ptt) REVERT: D 240 GLN cc_start: 0.8287 (mp-120) cc_final: 0.7745 (mp10) outliers start: 36 outliers final: 24 residues processed: 156 average time/residue: 0.2506 time to fit residues: 63.0156 Evaluate side-chains 156 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS B 492 HIS C 492 HIS D 492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.114609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.100870 restraints weight = 21473.601| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 0.95 r_work: 0.2943 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17040 Z= 0.115 Angle : 0.535 6.141 23240 Z= 0.260 Chirality : 0.043 0.153 2348 Planarity : 0.004 0.052 3080 Dihedral : 7.007 72.642 2272 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.97 % Allowed : 10.07 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.68 (0.19), residues: 2000 helix: 1.40 (0.20), residues: 708 sheet: 0.62 (0.31), residues: 288 loop : -0.23 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 183 HIS 0.004 0.001 HIS C 235 PHE 0.011 0.001 PHE D 136 TYR 0.017 0.001 TYR C 236 ARG 0.002 0.000 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 672) hydrogen bonds : angle 5.34610 ( 1860) covalent geometry : bond 0.00286 (17036) covalent geometry : angle 0.53515 (23240) Misc. bond : bond 0.00434 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.8482 (mmm) cc_final: 0.8211 (mmm) REVERT: B 350 MET cc_start: 0.8504 (mmm) cc_final: 0.8232 (mmm) REVERT: C 212 MET cc_start: 0.8892 (ptt) cc_final: 0.8678 (ptt) REVERT: C 350 MET cc_start: 0.8531 (mmm) cc_final: 0.8251 (mmm) REVERT: D 350 MET cc_start: 0.8509 (mmm) cc_final: 0.8233 (mmm) outliers start: 34 outliers final: 12 residues processed: 180 average time/residue: 0.2659 time to fit residues: 75.5381 Evaluate side-chains 146 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 188 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 112 optimal weight: 0.0470 chunk 176 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 95 optimal weight: 0.0770 chunk 171 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 81 optimal weight: 0.0970 chunk 27 optimal weight: 5.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN B 471 GLN C 471 GLN D 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.104126 restraints weight = 21164.659| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 0.90 r_work: 0.2995 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17040 Z= 0.092 Angle : 0.516 6.274 23240 Z= 0.249 Chirality : 0.042 0.153 2348 Planarity : 0.004 0.048 3080 Dihedral : 6.738 68.520 2272 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.68 % Allowed : 11.52 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.91 (0.19), residues: 2000 helix: 1.63 (0.20), residues: 704 sheet: 0.72 (0.30), residues: 288 loop : -0.11 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 183 HIS 0.004 0.001 HIS A 235 PHE 0.012 0.001 PHE D 57 TYR 0.014 0.001 TYR A 236 ARG 0.004 0.000 ARG C 354 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 672) hydrogen bonds : angle 5.10535 ( 1860) covalent geometry : bond 0.00219 (17036) covalent geometry : angle 0.51639 (23240) Misc. bond : bond 0.02192 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 212 MET cc_start: 0.8787 (ptt) cc_final: 0.8561 (ptt) REVERT: C 350 MET cc_start: 0.8377 (mmm) cc_final: 0.8064 (mmm) REVERT: D 350 MET cc_start: 0.8354 (mmm) cc_final: 0.8048 (mmm) outliers start: 29 outliers final: 24 residues processed: 173 average time/residue: 0.2470 time to fit residues: 68.7534 Evaluate side-chains 180 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 255 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 58 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 190 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.099848 restraints weight = 21448.667| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 0.92 r_work: 0.2919 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17040 Z= 0.173 Angle : 0.577 6.529 23240 Z= 0.284 Chirality : 0.045 0.149 2348 Planarity : 0.005 0.049 3080 Dihedral : 6.967 71.376 2272 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.26 % Allowed : 11.63 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2000 helix: 1.46 (0.19), residues: 716 sheet: 0.45 (0.30), residues: 288 loop : -0.38 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 183 HIS 0.004 0.001 HIS D 235 PHE 0.013 0.002 PHE D 136 TYR 0.019 0.002 TYR D 236 ARG 0.005 0.000 ARG C 354 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 672) hydrogen bonds : angle 5.34341 ( 1860) covalent geometry : bond 0.00437 (17036) covalent geometry : angle 0.57665 (23240) Misc. bond : bond 0.04202 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 2.067 Fit side-chains REVERT: A 240 GLN cc_start: 0.8265 (mp-120) cc_final: 0.7706 (mp10) REVERT: A 350 MET cc_start: 0.8448 (mmm) cc_final: 0.8188 (mtp) REVERT: B 240 GLN cc_start: 0.8251 (mp-120) cc_final: 0.7698 (mp10) REVERT: B 350 MET cc_start: 0.8467 (mmm) cc_final: 0.8213 (mtp) REVERT: C 240 GLN cc_start: 0.8249 (mp-120) cc_final: 0.7696 (mp10) REVERT: D 240 GLN cc_start: 0.8253 (mp-120) cc_final: 0.7699 (mp10) outliers start: 39 outliers final: 27 residues processed: 163 average time/residue: 0.2505 time to fit residues: 65.6494 Evaluate side-chains 171 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 496 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 141 optimal weight: 0.2980 chunk 105 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 83 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.115692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.102660 restraints weight = 21232.307| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 0.92 r_work: 0.2963 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17040 Z= 0.110 Angle : 0.529 6.272 23240 Z= 0.259 Chirality : 0.042 0.152 2348 Planarity : 0.004 0.050 3080 Dihedral : 6.734 68.063 2272 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.91 % Allowed : 11.52 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 2000 helix: 1.59 (0.19), residues: 716 sheet: 0.51 (0.30), residues: 288 loop : -0.30 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 183 HIS 0.004 0.001 HIS A 235 PHE 0.012 0.001 PHE B 57 TYR 0.016 0.001 TYR D 236 ARG 0.005 0.000 ARG D 354 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 672) hydrogen bonds : angle 5.15977 ( 1860) covalent geometry : bond 0.00276 (17036) covalent geometry : angle 0.52915 (23240) Misc. bond : bond 0.00900 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 TYR cc_start: 0.8581 (m-80) cc_final: 0.8300 (m-80) REVERT: B 425 TYR cc_start: 0.8583 (m-80) cc_final: 0.8300 (m-80) REVERT: C 61 MET cc_start: 0.7923 (mmt) cc_final: 0.7655 (mmt) REVERT: D 61 MET cc_start: 0.7947 (mmt) cc_final: 0.7684 (mmt) outliers start: 33 outliers final: 32 residues processed: 173 average time/residue: 0.2691 time to fit residues: 75.0642 Evaluate side-chains 176 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 255 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 chunk 27 optimal weight: 0.0870 chunk 105 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.104413 restraints weight = 21143.256| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 0.92 r_work: 0.3000 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17040 Z= 0.098 Angle : 0.527 8.007 23240 Z= 0.255 Chirality : 0.042 0.152 2348 Planarity : 0.004 0.049 3080 Dihedral : 6.598 64.485 2272 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.68 % Allowed : 12.21 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.84 (0.19), residues: 2000 helix: 1.62 (0.19), residues: 716 sheet: 0.69 (0.30), residues: 288 loop : -0.22 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 183 HIS 0.004 0.001 HIS C 235 PHE 0.019 0.001 PHE B 57 TYR 0.015 0.001 TYR D 236 ARG 0.003 0.000 ARG C 354 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 672) hydrogen bonds : angle 5.03878 ( 1860) covalent geometry : bond 0.00236 (17036) covalent geometry : angle 0.52741 (23240) Misc. bond : bond 0.00072 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: 0.7928 (mmt) cc_final: 0.7686 (mmt) REVERT: D 61 MET cc_start: 0.7963 (mmt) cc_final: 0.7729 (mmt) outliers start: 29 outliers final: 27 residues processed: 174 average time/residue: 0.2505 time to fit residues: 70.2828 Evaluate side-chains 173 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 255 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 105 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 185 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 145 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.118299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.105365 restraints weight = 21288.172| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 0.93 r_work: 0.3006 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17040 Z= 0.102 Angle : 0.544 9.506 23240 Z= 0.263 Chirality : 0.042 0.151 2348 Planarity : 0.004 0.050 3080 Dihedral : 6.510 61.440 2272 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.74 % Allowed : 12.62 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.87 (0.19), residues: 2000 helix: 1.57 (0.20), residues: 720 sheet: 0.76 (0.31), residues: 288 loop : -0.17 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 183 HIS 0.004 0.001 HIS C 235 PHE 0.014 0.001 PHE B 57 TYR 0.015 0.001 TYR A 236 ARG 0.003 0.000 ARG A 354 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 672) hydrogen bonds : angle 4.98659 ( 1860) covalent geometry : bond 0.00247 (17036) covalent geometry : angle 0.54374 (23240) Misc. bond : bond 0.00436 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ASP cc_start: 0.7304 (t0) cc_final: 0.7101 (t0) REVERT: C 61 MET cc_start: 0.7979 (mmt) cc_final: 0.7682 (mmt) REVERT: D 61 MET cc_start: 0.7977 (mmt) cc_final: 0.7676 (mmt) outliers start: 30 outliers final: 25 residues processed: 163 average time/residue: 0.2405 time to fit residues: 63.6282 Evaluate side-chains 174 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 255 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 134 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN B 324 ASN C 324 ASN D 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.101008 restraints weight = 21480.838| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.01 r_work: 0.2946 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17040 Z= 0.150 Angle : 0.582 9.497 23240 Z= 0.284 Chirality : 0.044 0.149 2348 Planarity : 0.005 0.050 3080 Dihedral : 6.737 64.104 2272 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.56 % Allowed : 13.37 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.77 (0.19), residues: 2000 helix: 1.59 (0.20), residues: 692 sheet: 0.90 (0.32), residues: 260 loop : -0.30 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 183 HIS 0.004 0.001 HIS B 235 PHE 0.013 0.001 PHE B 57 TYR 0.019 0.002 TYR D 236 ARG 0.004 0.000 ARG B 354 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 672) hydrogen bonds : angle 5.21013 ( 1860) covalent geometry : bond 0.00376 (17036) covalent geometry : angle 0.58180 (23240) Misc. bond : bond 0.03406 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6833.20 seconds wall clock time: 119 minutes 31.61 seconds (7171.61 seconds total)