Starting phenix.real_space_refine on Sat Jun 14 23:42:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvd_17962/06_2025/8pvd_17962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvd_17962/06_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_17962/06_2025/8pvd_17962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvd_17962/06_2025/8pvd_17962.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvd_17962/06_2025/8pvd_17962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvd_17962/06_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-5710/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: 9.39, per 1000 atoms: 0.57 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: 4.22 Conformation dependent library (CDL) restraints added in 2.1 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: 1.70 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: 4.96 Time building geometry restraints manager: 4.95 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: 0.13 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: 1.230 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: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.520 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.730 ------------------------------------------------------------------------------- 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 : 1.779 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: 0.3495 time to fit residues: 167.6950 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 : 1.784 ------------------------------------------------------------------------------- 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 = 62)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.101342 restraints weight = 20642.209| |-----------------------------------------------------------------------------| 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: 0.2803 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 5.486 23240 Z= 0.300 Chirality : 0.044 0.156 2348 Planarity : 0.004 0.033 3080 Dihedral : 7.756 79.871 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 5.78724 ( 1860) covalent geometry : bond 0.00278 (17036) covalent geometry : angle 0.58388 (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 : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8673 (ptt) cc_final: 0.8464 (ptt) REVERT: A 293 PRO cc_start: 0.8429 (Cg_exo) cc_final: 0.8182 (Cg_endo) REVERT: A 350 MET cc_start: 0.8497 (mmm) cc_final: 0.8260 (mmm) REVERT: A 428 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7152 (mp0) REVERT: A 453 GLU cc_start: 0.5587 (mm-30) cc_final: 0.5386 (mm-30) REVERT: A 457 LYS cc_start: 0.7320 (tttm) cc_final: 0.7088 (mptt) REVERT: B 212 MET cc_start: 0.8676 (ptt) cc_final: 0.8470 (ptt) REVERT: B 293 PRO cc_start: 0.8433 (Cg_exo) cc_final: 0.8185 (Cg_endo) REVERT: B 350 MET cc_start: 0.8532 (mmm) cc_final: 0.8295 (mmm) REVERT: B 428 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7137 (mp0) REVERT: B 453 GLU cc_start: 0.5589 (mm-30) cc_final: 0.5373 (mm-30) REVERT: B 457 LYS cc_start: 0.7304 (tttm) cc_final: 0.7047 (mptt) REVERT: C 212 MET cc_start: 0.8691 (ptt) cc_final: 0.8487 (ptt) REVERT: C 293 PRO cc_start: 0.8424 (Cg_exo) cc_final: 0.8174 (Cg_endo) REVERT: C 350 MET cc_start: 0.8512 (mmm) cc_final: 0.8257 (mmm) REVERT: C 424 GLN cc_start: 0.7219 (tt0) cc_final: 0.6651 (mp10) REVERT: C 453 GLU cc_start: 0.5592 (mm-30) cc_final: 0.5376 (mm-30) REVERT: C 457 LYS cc_start: 0.7321 (tttm) cc_final: 0.7076 (mptt) REVERT: D 212 MET cc_start: 0.8690 (ptt) cc_final: 0.8475 (ptt) REVERT: D 293 PRO cc_start: 0.8433 (Cg_exo) cc_final: 0.8185 (Cg_endo) REVERT: D 350 MET cc_start: 0.8520 (mmm) cc_final: 0.8273 (mmm) REVERT: D 424 GLN cc_start: 0.7269 (tt0) cc_final: 0.6691 (mp10) REVERT: D 453 GLU cc_start: 0.5585 (mm-30) cc_final: 0.5372 (mm-30) REVERT: D 457 LYS cc_start: 0.7308 (tttm) cc_final: 0.7062 (mptt) outliers start: 26 outliers final: 18 residues processed: 194 average time/residue: 0.2818 time to fit residues: 83.7979 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 : 1.923 ------------------------------------------------------------------------------- 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: 0.8980 chunk 192 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 187 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 71 optimal weight: 0.3980 chunk 183 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.118774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.104490 restraints weight = 20363.694| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 0.97 r_work: 0.2905 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17040 Z= 0.121 Angle : 0.562 6.030 23240 Z= 0.275 Chirality : 0.044 0.153 2348 Planarity : 0.004 0.040 3080 Dihedral : 7.142 75.831 2272 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.62 % Allowed : 9.14 % Favored : 89.24 % 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: 0.82 (0.19), residues: 2000 helix: 1.47 (0.19), residues: 724 sheet: 0.73 (0.29), residues: 308 loop : -0.16 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 183 HIS 0.003 0.001 HIS C 235 PHE 0.012 0.002 PHE A 57 TYR 0.017 0.001 TYR B 236 ARG 0.003 0.000 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 672) hydrogen bonds : angle 5.40133 ( 1860) covalent geometry : bond 0.00300 (17036) covalent geometry : angle 0.56188 (23240) Misc. bond : bond 0.00720 ( 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 204 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 1.960 Fit side-chains REVERT: A 212 MET cc_start: 0.8800 (ptt) cc_final: 0.8545 (ptt) REVERT: A 240 GLN cc_start: 0.8232 (mp-120) cc_final: 0.7692 (mp10) REVERT: A 350 MET cc_start: 0.8440 (mmm) cc_final: 0.8137 (mmm) REVERT: A 439 ASN cc_start: 0.7652 (m-40) cc_final: 0.7416 (m110) REVERT: B 212 MET cc_start: 0.8788 (ptt) cc_final: 0.8533 (ptt) REVERT: B 240 GLN cc_start: 0.8235 (mp-120) cc_final: 0.7691 (mp10) REVERT: B 350 MET cc_start: 0.8460 (mmm) cc_final: 0.8163 (mmm) REVERT: B 439 ASN cc_start: 0.7678 (m-40) cc_final: 0.7435 (m110) REVERT: C 212 MET cc_start: 0.8798 (ptt) cc_final: 0.8550 (ptt) REVERT: C 240 GLN cc_start: 0.8244 (mp-120) cc_final: 0.7706 (mp10) REVERT: C 350 MET cc_start: 0.8473 (mmm) cc_final: 0.8155 (mmm) REVERT: C 439 ASN cc_start: 0.7672 (m-40) cc_final: 0.7438 (m110) REVERT: D 212 MET cc_start: 0.8797 (ptt) cc_final: 0.8538 (ptt) REVERT: D 240 GLN cc_start: 0.8234 (mp-120) cc_final: 0.7693 (mp10) REVERT: D 350 MET cc_start: 0.8468 (mmm) cc_final: 0.8157 (mmm) REVERT: D 439 ASN cc_start: 0.7680 (m-40) cc_final: 0.7435 (m110) outliers start: 28 outliers final: 12 residues processed: 188 average time/residue: 0.2793 time to fit residues: 81.2492 Evaluate side-chains 156 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 2.016 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 37 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS A 471 GLN A 492 HIS B 372 HIS B 471 GLN B 492 HIS C 372 HIS C 471 GLN C 492 HIS D 372 HIS D 471 GLN D 492 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.104791 restraints weight = 20980.129| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 0.90 r_work: 0.2993 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17040 Z= 0.095 Angle : 0.523 6.029 23240 Z= 0.252 Chirality : 0.042 0.154 2348 Planarity : 0.004 0.048 3080 Dihedral : 6.897 72.444 2272 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.74 % Allowed : 9.61 % Favored : 88.66 % 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: 0.99 (0.19), residues: 2000 helix: 1.58 (0.20), residues: 708 sheet: 0.71 (0.30), residues: 312 loop : 0.04 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 183 HIS 0.004 0.000 HIS A 235 PHE 0.010 0.001 PHE A 136 TYR 0.015 0.001 TYR B 236 ARG 0.002 0.000 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 672) hydrogen bonds : angle 5.19004 ( 1860) covalent geometry : bond 0.00230 (17036) covalent geometry : angle 0.52303 (23240) Misc. bond : bond 0.01134 ( 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 200 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8775 (ptt) cc_final: 0.8507 (ptt) REVERT: B 212 MET cc_start: 0.8758 (ptt) cc_final: 0.8491 (ptt) REVERT: C 212 MET cc_start: 0.8773 (ptt) cc_final: 0.8511 (ptt) REVERT: D 212 MET cc_start: 0.8771 (ptt) cc_final: 0.8506 (ptt) outliers start: 30 outliers final: 16 residues processed: 188 average time/residue: 0.2621 time to fit residues: 77.9713 Evaluate side-chains 162 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.906 ------------------------------------------------------------------------------- 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 A residue 255 GLN 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 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 D residue 51 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 40 optimal weight: 0.0570 chunk 8 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 141 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.117590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105560 restraints weight = 21180.877| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 0.83 r_work: 0.2970 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3269 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= 0.103 Angle : 0.535 7.146 23240 Z= 0.253 Chirality : 0.042 0.153 2348 Planarity : 0.004 0.046 3080 Dihedral : 6.774 70.315 2272 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.39 % Allowed : 9.95 % Favored : 88.66 % 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: 1.04 (0.19), residues: 2000 helix: 1.56 (0.20), residues: 708 sheet: 0.84 (0.30), residues: 308 loop : 0.09 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 183 HIS 0.004 0.001 HIS A 235 PHE 0.011 0.001 PHE C 136 TYR 0.016 0.001 TYR B 236 ARG 0.002 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 672) hydrogen bonds : angle 5.12031 ( 1860) covalent geometry : bond 0.00252 (17036) covalent geometry : angle 0.53544 (23240) Misc. bond : bond 0.01217 ( 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 176 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8740 (ptt) cc_final: 0.8515 (ptt) REVERT: B 212 MET cc_start: 0.8741 (ptt) cc_final: 0.8520 (ptt) REVERT: C 212 MET cc_start: 0.8747 (ptt) cc_final: 0.8528 (ptt) REVERT: D 212 MET cc_start: 0.8742 (ptt) cc_final: 0.8508 (ptt) outliers start: 24 outliers final: 14 residues processed: 166 average time/residue: 0.2826 time to fit residues: 73.1333 Evaluate side-chains 154 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 A residue 255 GLN 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 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: 6.9990 chunk 128 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 chunk 176 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.115850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.102710 restraints weight = 21283.504| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 0.92 r_work: 0.2967 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17040 Z= 0.126 Angle : 0.545 6.219 23240 Z= 0.266 Chirality : 0.043 0.152 2348 Planarity : 0.004 0.045 3080 Dihedral : 6.810 69.714 2272 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.27 % Allowed : 10.76 % 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: 0.97 (0.19), residues: 2000 helix: 1.57 (0.20), residues: 708 sheet: 0.68 (0.30), residues: 308 loop : 0.04 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 183 HIS 0.004 0.001 HIS A 235 PHE 0.019 0.001 PHE B 57 TYR 0.017 0.001 TYR B 236 ARG 0.006 0.000 ARG C 430 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 672) hydrogen bonds : angle 5.16359 ( 1860) covalent geometry : bond 0.00315 (17036) covalent geometry : angle 0.54488 (23240) Misc. bond : bond 0.01672 ( 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 191 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 2.081 Fit side-chains REVERT: A 212 MET cc_start: 0.8815 (ptt) cc_final: 0.8561 (ptt) REVERT: A 240 GLN cc_start: 0.8183 (mp-120) cc_final: 0.7659 (mp10) REVERT: A 350 MET cc_start: 0.8328 (mtp) cc_final: 0.8062 (mtp) REVERT: B 212 MET cc_start: 0.8807 (ptt) cc_final: 0.8555 (ptt) REVERT: B 240 GLN cc_start: 0.8169 (mp-120) cc_final: 0.7650 (mp10) REVERT: B 350 MET cc_start: 0.8338 (mtp) cc_final: 0.8070 (mtp) REVERT: C 212 MET cc_start: 0.8800 (ptt) cc_final: 0.8553 (ptt) REVERT: C 240 GLN cc_start: 0.8176 (mp-120) cc_final: 0.7656 (mp10) REVERT: C 350 MET cc_start: 0.8318 (mtp) cc_final: 0.8046 (mtp) REVERT: D 212 MET cc_start: 0.8807 (ptt) cc_final: 0.8550 (ptt) REVERT: D 240 GLN cc_start: 0.8183 (mp-120) cc_final: 0.7657 (mp10) REVERT: D 350 MET cc_start: 0.8270 (mtp) cc_final: 0.7992 (mtp) outliers start: 22 outliers final: 14 residues processed: 177 average time/residue: 0.3070 time to fit residues: 88.1274 Evaluate side-chains 166 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 2.283 ------------------------------------------------------------------------------- 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 A residue 255 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 162 optimal weight: 0.0170 chunk 165 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 158 optimal weight: 0.0270 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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 = 0.3272 r_free = 0.3272 target = 0.118083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104781 restraints weight = 21078.416| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 0.94 r_work: 0.3001 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17040 Z= 0.095 Angle : 0.515 6.193 23240 Z= 0.251 Chirality : 0.042 0.152 2348 Planarity : 0.004 0.044 3080 Dihedral : 6.542 65.114 2272 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.16 % Allowed : 11.69 % Favored : 87.15 % 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: 1.08 (0.19), residues: 2000 helix: 1.75 (0.20), residues: 716 sheet: 0.78 (0.30), residues: 308 loop : -0.01 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 183 HIS 0.004 0.001 HIS C 235 PHE 0.014 0.001 PHE D 57 TYR 0.014 0.001 TYR D 236 ARG 0.006 0.000 ARG C 430 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 672) hydrogen bonds : angle 4.99034 ( 1860) covalent geometry : bond 0.00228 (17036) covalent geometry : angle 0.51518 (23240) Misc. bond : bond 0.00858 ( 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 186 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7896 (tpp) cc_final: 0.7607 (mtp) REVERT: A 212 MET cc_start: 0.8798 (ptt) cc_final: 0.8550 (ptt) REVERT: A 350 MET cc_start: 0.8208 (mtp) cc_final: 0.7967 (mtp) REVERT: B 61 MET cc_start: 0.7874 (tpp) cc_final: 0.7609 (mtp) REVERT: B 212 MET cc_start: 0.8796 (ptt) cc_final: 0.8547 (ptt) REVERT: B 350 MET cc_start: 0.8233 (mtp) cc_final: 0.7999 (mtp) REVERT: C 212 MET cc_start: 0.8781 (ptt) cc_final: 0.8528 (ptt) REVERT: C 257 ASP cc_start: 0.7407 (t0) cc_final: 0.7138 (p0) REVERT: D 212 MET cc_start: 0.8781 (ptt) cc_final: 0.8522 (ptt) REVERT: D 257 ASP cc_start: 0.7395 (t0) cc_final: 0.7136 (p0) outliers start: 20 outliers final: 16 residues processed: 170 average time/residue: 0.2583 time to fit residues: 70.6452 Evaluate side-chains 168 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.942 ------------------------------------------------------------------------------- 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 A residue 255 GLN 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 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 52 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 141 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.101939 restraints weight = 21353.277| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.04 r_work: 0.2956 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17040 Z= 0.118 Angle : 0.533 6.369 23240 Z= 0.261 Chirality : 0.042 0.150 2348 Planarity : 0.004 0.045 3080 Dihedral : 6.593 64.010 2272 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.39 % Allowed : 11.23 % Favored : 87.38 % 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: 1.08 (0.19), residues: 2000 helix: 1.74 (0.20), residues: 700 sheet: 0.82 (0.31), residues: 288 loop : 0.03 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.004 0.001 HIS A 235 PHE 0.012 0.001 PHE D 57 TYR 0.016 0.001 TYR B 236 ARG 0.005 0.000 ARG C 430 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 672) hydrogen bonds : angle 5.05780 ( 1860) covalent geometry : bond 0.00294 (17036) covalent geometry : angle 0.53272 (23240) Misc. bond : bond 0.01903 ( 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 188 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.964 Fit side-chains REVERT: A 212 MET cc_start: 0.8887 (ptt) cc_final: 0.8635 (ptt) REVERT: A 240 GLN cc_start: 0.8214 (mp-120) cc_final: 0.7717 (mp10) REVERT: A 257 ASP cc_start: 0.7522 (t0) cc_final: 0.7179 (p0) REVERT: B 212 MET cc_start: 0.8882 (ptt) cc_final: 0.8627 (ptt) REVERT: B 240 GLN cc_start: 0.8202 (mp-120) cc_final: 0.7694 (mp10) REVERT: B 257 ASP cc_start: 0.7540 (t0) cc_final: 0.7195 (p0) REVERT: C 212 MET cc_start: 0.8858 (ptt) cc_final: 0.8608 (ptt) REVERT: C 240 GLN cc_start: 0.8219 (mp-120) cc_final: 0.7718 (mp10) REVERT: C 257 ASP cc_start: 0.7487 (t0) cc_final: 0.7165 (p0) REVERT: D 212 MET cc_start: 0.8870 (ptt) cc_final: 0.8615 (ptt) REVERT: D 240 GLN cc_start: 0.8219 (mp-120) cc_final: 0.7721 (mp10) REVERT: D 257 ASP cc_start: 0.7478 (t0) cc_final: 0.7152 (p0) outliers start: 24 outliers final: 20 residues processed: 168 average time/residue: 0.2702 time to fit residues: 73.1601 Evaluate side-chains 174 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 1.878 ------------------------------------------------------------------------------- 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 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 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 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 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: 7.9990 chunk 61 optimal weight: 7.9990 chunk 152 optimal weight: 0.0770 chunk 192 optimal weight: 0.0870 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 75 optimal weight: 0.0970 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 397 ASN C 397 ASN D 397 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.119741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106174 restraints weight = 21211.280| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.00 r_work: 0.3014 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17040 Z= 0.090 Angle : 0.515 7.030 23240 Z= 0.248 Chirality : 0.041 0.152 2348 Planarity : 0.004 0.046 3080 Dihedral : 6.315 60.740 2272 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.39 % Allowed : 11.69 % Favored : 86.92 % 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: 1.15 (0.19), residues: 2000 helix: 1.73 (0.20), residues: 716 sheet: 0.90 (0.30), residues: 308 loop : 0.06 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.004 0.000 HIS C 235 PHE 0.017 0.001 PHE A 57 TYR 0.013 0.001 TYR D 236 ARG 0.005 0.000 ARG D 430 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 672) hydrogen bonds : angle 4.86482 ( 1860) covalent geometry : bond 0.00213 (17036) covalent geometry : angle 0.51539 (23240) Misc. bond : bond 0.01650 ( 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 195 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7376 (t0) cc_final: 0.7115 (p0) REVERT: A 212 MET cc_start: 0.8805 (ptt) cc_final: 0.8574 (ptt) REVERT: A 257 ASP cc_start: 0.7536 (t0) cc_final: 0.7222 (p0) REVERT: B 54 ASP cc_start: 0.7391 (t0) cc_final: 0.7119 (p0) REVERT: B 212 MET cc_start: 0.8796 (ptt) cc_final: 0.8564 (ptt) REVERT: B 257 ASP cc_start: 0.7530 (t0) cc_final: 0.7217 (p0) REVERT: C 61 MET cc_start: 0.7946 (mtp) cc_final: 0.7737 (mtp) REVERT: C 212 MET cc_start: 0.8775 (ptt) cc_final: 0.8549 (ptt) REVERT: C 257 ASP cc_start: 0.7450 (t0) cc_final: 0.7177 (p0) REVERT: D 61 MET cc_start: 0.7909 (mtp) cc_final: 0.7698 (mtp) REVERT: D 212 MET cc_start: 0.8794 (ptt) cc_final: 0.8558 (ptt) REVERT: D 257 ASP cc_start: 0.7439 (t0) cc_final: 0.7162 (p0) outliers start: 24 outliers final: 24 residues processed: 175 average time/residue: 0.2477 time to fit residues: 69.7394 Evaluate side-chains 188 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 128 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 52 VAL 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 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 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 52 VAL Chi-restraints excluded: chain D residue 128 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: 2.9990 chunk 12 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.117867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.103496 restraints weight = 21388.904| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.08 r_work: 0.2970 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17040 Z= 0.107 Angle : 0.543 8.630 23240 Z= 0.260 Chirality : 0.042 0.151 2348 Planarity : 0.004 0.046 3080 Dihedral : 6.377 61.221 2272 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.39 % Allowed : 11.92 % Favored : 86.69 % 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: 1.12 (0.19), residues: 2000 helix: 1.72 (0.20), residues: 700 sheet: 0.92 (0.31), residues: 288 loop : 0.07 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.004 0.001 HIS B 235 PHE 0.013 0.001 PHE C 57 TYR 0.015 0.001 TYR C 236 ARG 0.005 0.000 ARG C 430 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 672) hydrogen bonds : angle 4.92303 ( 1860) covalent geometry : bond 0.00261 (17036) covalent geometry : angle 0.54271 (23240) Misc. bond : bond 0.01058 ( 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 186 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.970 Fit side-chains REVERT: A 54 ASP cc_start: 0.7440 (t0) cc_final: 0.7161 (p0) REVERT: A 212 MET cc_start: 0.8840 (ptt) cc_final: 0.8596 (ptt) REVERT: A 240 GLN cc_start: 0.8206 (mp-120) cc_final: 0.7683 (mp10) REVERT: A 257 ASP cc_start: 0.7568 (t0) cc_final: 0.7224 (p0) REVERT: B 54 ASP cc_start: 0.7447 (t0) cc_final: 0.7170 (p0) REVERT: B 212 MET cc_start: 0.8825 (ptt) cc_final: 0.8577 (ptt) REVERT: B 240 GLN cc_start: 0.8190 (mp-120) cc_final: 0.7659 (mp10) REVERT: B 257 ASP cc_start: 0.7593 (t0) cc_final: 0.7237 (p0) REVERT: C 212 MET cc_start: 0.8813 (ptt) cc_final: 0.8568 (ptt) REVERT: C 240 GLN cc_start: 0.8206 (mp-120) cc_final: 0.7696 (mp10) REVERT: C 257 ASP cc_start: 0.7549 (t0) cc_final: 0.7277 (p0) REVERT: D 212 MET cc_start: 0.8820 (ptt) cc_final: 0.8567 (ptt) REVERT: D 240 GLN cc_start: 0.8211 (mp-120) cc_final: 0.7700 (mp10) REVERT: D 257 ASP cc_start: 0.7543 (t0) cc_final: 0.7260 (p0) outliers start: 24 outliers final: 20 residues processed: 166 average time/residue: 0.3334 time to fit residues: 89.6963 Evaluate side-chains 180 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 2.595 ------------------------------------------------------------------------------- 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 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 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 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 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: 10.0000 chunk 189 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 116 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 158 optimal weight: 0.0060 chunk 118 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 324 ASN ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN D 324 ASN ** D 397 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 = 0.3279 r_free = 0.3279 target = 0.119099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.105652 restraints weight = 21256.752| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 0.99 r_work: 0.3011 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3850 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= 0.097 Angle : 0.540 8.990 23240 Z= 0.257 Chirality : 0.041 0.152 2348 Planarity : 0.004 0.046 3080 Dihedral : 6.263 61.226 2272 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.27 % Allowed : 11.92 % 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: 1.22 (0.19), residues: 2000 helix: 1.78 (0.20), residues: 696 sheet: 0.97 (0.31), residues: 288 loop : 0.15 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 183 HIS 0.004 0.001 HIS C 235 PHE 0.021 0.001 PHE B 57 TYR 0.014 0.001 TYR A 236 ARG 0.005 0.000 ARG C 430 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 672) hydrogen bonds : angle 4.86470 ( 1860) covalent geometry : bond 0.00234 (17036) covalent geometry : angle 0.54021 (23240) Misc. bond : bond 0.01145 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8051.07 seconds wall clock time: 142 minutes 32.73 seconds (8552.73 seconds total)