Starting phenix.real_space_refine on Sun Aug 24 03:34:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvd_17962/08_2025/8pvd_17962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvd_17962/08_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_17962/08_2025/8pvd_17962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvd_17962/08_2025/8pvd_17962.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvd_17962/08_2025/8pvd_17962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvd_17962/08_2025/8pvd_17962.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: B, C, D Time building chain proxies: 3.94, per 1000 atoms: 0.24 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: 1.42 Conformation dependent library (CDL) restraints added in 785.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.60 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: 2.78 Time building geometry restraints manager: 1.86 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.100 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.060 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (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 ARG 0.038 0.006 ARG B 68 TYR 0.052 0.009 TYR B 137 PHE 0.048 0.009 PHE B 334 TRP 0.031 0.007 TRP B 277 HIS 0.018 0.004 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.01198 (17036) covalent geometry : angle 1.85213 (23240) hydrogen bonds : bond 0.20555 ( 672) hydrogen bonds : angle 8.46253 ( 1860) 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 : 0.667 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: 0.1728 time to fit residues: 83.1361 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 : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3221 r_free = 0.3221 target = 0.115344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.100325 restraints weight = 20702.172| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.00 r_work: 0.2897 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17040 Z= 0.133 Angle : 0.595 5.621 23240 Z= 0.305 Chirality : 0.045 0.153 2348 Planarity : 0.004 0.034 3080 Dihedral : 7.699 79.620 2272 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.80 % Favored : 97.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.18), residues: 2000 helix: 1.10 (0.19), residues: 712 sheet: 0.43 (0.27), residues: 332 loop : -0.17 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 72 TYR 0.021 0.001 TYR B 236 PHE 0.011 0.001 PHE A 154 TRP 0.009 0.002 TRP A 277 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00321 (17036) covalent geometry : angle 0.59534 (23240) hydrogen bonds : bond 0.04415 ( 672) hydrogen bonds : angle 5.80778 ( 1860) Misc. bond : bond 0.00642 ( 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 194 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8736 (ptt) cc_final: 0.8506 (ptt) REVERT: A 293 PRO cc_start: 0.8466 (Cg_exo) cc_final: 0.8226 (Cg_endo) REVERT: A 350 MET cc_start: 0.8517 (mmm) cc_final: 0.8272 (mmm) REVERT: A 428 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7174 (mp0) REVERT: A 457 LYS cc_start: 0.7349 (tttm) cc_final: 0.6980 (mptt) REVERT: B 212 MET cc_start: 0.8735 (ptt) cc_final: 0.8507 (ptt) REVERT: B 293 PRO cc_start: 0.8470 (Cg_exo) cc_final: 0.8232 (Cg_endo) REVERT: B 350 MET cc_start: 0.8556 (mmm) cc_final: 0.8311 (mmm) REVERT: B 428 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7160 (mp0) REVERT: B 457 LYS cc_start: 0.7327 (tttm) cc_final: 0.6941 (mptt) REVERT: C 212 MET cc_start: 0.8748 (ptt) cc_final: 0.8526 (ptt) REVERT: C 293 PRO cc_start: 0.8458 (Cg_exo) cc_final: 0.8216 (Cg_endo) REVERT: C 350 MET cc_start: 0.8538 (mmm) cc_final: 0.8279 (mmm) REVERT: C 424 GLN cc_start: 0.7284 (tt0) cc_final: 0.6660 (mp10) REVERT: C 457 LYS cc_start: 0.7341 (tttm) cc_final: 0.6959 (mptt) REVERT: D 212 MET cc_start: 0.8747 (ptt) cc_final: 0.8516 (ptt) REVERT: D 293 PRO cc_start: 0.8475 (Cg_exo) cc_final: 0.8237 (Cg_endo) REVERT: D 350 MET cc_start: 0.8518 (mmm) cc_final: 0.8264 (mmm) REVERT: D 424 GLN cc_start: 0.7309 (tt0) cc_final: 0.6689 (mp10) REVERT: D 457 LYS cc_start: 0.7336 (tttm) cc_final: 0.6958 (mptt) outliers start: 26 outliers final: 18 residues processed: 182 average time/residue: 0.1305 time to fit residues: 37.1616 Evaluate side-chains 157 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 152 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 372 HIS C 372 HIS D 372 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.106775 restraints weight = 20617.056| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 0.97 r_work: 0.2929 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2718 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= 0.113 Angle : 0.548 5.972 23240 Z= 0.269 Chirality : 0.043 0.153 2348 Planarity : 0.004 0.041 3080 Dihedral : 7.105 75.456 2272 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.62 % Allowed : 8.45 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.19), residues: 2000 helix: 1.49 (0.19), residues: 724 sheet: 0.71 (0.29), residues: 308 loop : -0.16 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.016 0.001 TYR A 236 PHE 0.011 0.001 PHE D 136 TRP 0.008 0.001 TRP C 183 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00278 (17036) covalent geometry : angle 0.54795 (23240) hydrogen bonds : bond 0.03728 ( 672) hydrogen bonds : angle 5.37236 ( 1860) Misc. bond : bond 0.00161 ( 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 192 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8787 (ptt) cc_final: 0.8541 (ptt) REVERT: B 212 MET cc_start: 0.8780 (ptt) cc_final: 0.8537 (ptt) REVERT: B 439 ASN cc_start: 0.7708 (m-40) cc_final: 0.7433 (m110) REVERT: C 212 MET cc_start: 0.8805 (ptt) cc_final: 0.8565 (ptt) REVERT: C 255 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.6531 (pt0) REVERT: D 212 MET cc_start: 0.8799 (ptt) cc_final: 0.8549 (ptt) REVERT: D 255 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.6520 (pt0) REVERT: D 439 ASN cc_start: 0.7705 (m-40) cc_final: 0.7426 (m110) outliers start: 28 outliers final: 16 residues processed: 176 average time/residue: 0.1114 time to fit residues: 30.9242 Evaluate side-chains 152 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 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 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 255 GLN 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 Chi-restraints excluded: chain D residue 255 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 175 optimal weight: 0.0270 chunk 65 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 overall best weight: 3.2044 ------------------------------------------------------------------------------- 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 = 0.3161 r_free = 0.3161 target = 0.109794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.097110 restraints weight = 21790.724| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 0.97 r_work: 0.2857 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17040 Z= 0.251 Angle : 0.664 7.647 23240 Z= 0.327 Chirality : 0.048 0.149 2348 Planarity : 0.006 0.056 3080 Dihedral : 7.400 77.652 2272 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.18), residues: 2000 helix: 1.17 (0.19), residues: 700 sheet: 0.68 (0.30), residues: 284 loop : -0.39 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 72 TYR 0.022 0.002 TYR B 236 PHE 0.016 0.002 PHE C 294 TRP 0.008 0.002 TRP A 183 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00634 (17036) covalent geometry : angle 0.66386 (23240) hydrogen bonds : bond 0.04623 ( 672) hydrogen bonds : angle 5.81100 ( 1860) Misc. bond : bond 0.06075 ( 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 162 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.616 Fit side-chains REVERT: A 212 MET cc_start: 0.8951 (ptt) cc_final: 0.8719 (ptt) REVERT: A 240 GLN cc_start: 0.8356 (mp-120) cc_final: 0.7885 (mp10) REVERT: A 350 MET cc_start: 0.8643 (mmm) cc_final: 0.8387 (mmm) REVERT: B 212 MET cc_start: 0.8961 (ptt) cc_final: 0.8725 (ptt) REVERT: B 240 GLN cc_start: 0.8355 (mp-120) cc_final: 0.7877 (mp10) REVERT: B 350 MET cc_start: 0.8679 (mmm) cc_final: 0.8424 (mmm) REVERT: C 212 MET cc_start: 0.8954 (ptt) cc_final: 0.8727 (ptt) REVERT: C 350 MET cc_start: 0.8656 (mmm) cc_final: 0.8388 (mmm) REVERT: D 212 MET cc_start: 0.8953 (ptt) cc_final: 0.8711 (ptt) REVERT: D 350 MET cc_start: 0.8672 (mmm) cc_final: 0.8406 (mmm) outliers start: 30 outliers final: 22 residues processed: 150 average time/residue: 0.1142 time to fit residues: 27.4579 Evaluate side-chains 158 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 93 LYS 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 52 VAL Chi-restraints excluded: chain B residue 93 LYS 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 93 LYS 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 93 LYS 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 22 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 179 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.115174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.101954 restraints weight = 21376.996| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 0.93 r_work: 0.2956 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3287 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= 0.102 Angle : 0.533 6.039 23240 Z= 0.257 Chirality : 0.042 0.153 2348 Planarity : 0.004 0.052 3080 Dihedral : 6.923 72.934 2272 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.74 % Allowed : 10.07 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.19), residues: 2000 helix: 1.43 (0.20), residues: 708 sheet: 0.65 (0.30), residues: 288 loop : -0.11 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 72 TYR 0.016 0.001 TYR A 236 PHE 0.010 0.001 PHE A 136 TRP 0.009 0.001 TRP C 183 HIS 0.003 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00248 (17036) covalent geometry : angle 0.53284 (23240) hydrogen bonds : bond 0.03409 ( 672) hydrogen bonds : angle 5.34289 ( 1860) Misc. bond : bond 0.02605 ( 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 184 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 174 average time/residue: 0.1139 time to fit residues: 31.1150 Evaluate side-chains 150 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 126 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3178 r_free = 0.3178 target = 0.111063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.097766 restraints weight = 21624.786| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 0.94 r_work: 0.2897 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17040 Z= 0.206 Angle : 0.611 6.872 23240 Z= 0.302 Chirality : 0.046 0.150 2348 Planarity : 0.005 0.051 3080 Dihedral : 7.222 74.836 2272 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.56 % Allowed : 11.11 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.18), residues: 2000 helix: 1.28 (0.19), residues: 700 sheet: 0.39 (0.29), residues: 288 loop : -0.33 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 430 TYR 0.021 0.002 TYR C 236 PHE 0.014 0.002 PHE B 136 TRP 0.009 0.001 TRP D 183 HIS 0.005 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00521 (17036) covalent geometry : angle 0.61148 (23240) hydrogen bonds : bond 0.04233 ( 672) hydrogen bonds : angle 5.60591 ( 1860) Misc. bond : bond 0.05160 ( 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 168 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.488 Fit side-chains REVERT: A 240 GLN cc_start: 0.8334 (mp-120) cc_final: 0.7828 (mp10) REVERT: A 350 MET cc_start: 0.8583 (mmm) cc_final: 0.8233 (mtp) REVERT: B 240 GLN cc_start: 0.8324 (mp-120) cc_final: 0.7823 (mp10) REVERT: B 350 MET cc_start: 0.8588 (mmm) cc_final: 0.8237 (mtp) REVERT: C 240 GLN cc_start: 0.8340 (mp-120) cc_final: 0.7834 (mp10) REVERT: C 350 MET cc_start: 0.8525 (mmm) cc_final: 0.8152 (mtp) REVERT: D 240 GLN cc_start: 0.8336 (mp-120) cc_final: 0.7831 (mp10) REVERT: D 350 MET cc_start: 0.8513 (mmm) cc_final: 0.8146 (mtp) outliers start: 27 outliers final: 17 residues processed: 155 average time/residue: 0.1082 time to fit residues: 26.1912 Evaluate side-chains 150 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 496 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 496 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 496 LEU 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 496 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 97 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 12 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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 = 0.3212 r_free = 0.3212 target = 0.113613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.100592 restraints weight = 21508.985| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 0.92 r_work: 0.2941 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17040 Z= 0.128 Angle : 0.530 6.119 23240 Z= 0.264 Chirality : 0.043 0.152 2348 Planarity : 0.005 0.051 3080 Dihedral : 6.948 71.724 2272 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.91 % Allowed : 10.47 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.18), residues: 2000 helix: 1.50 (0.20), residues: 700 sheet: 0.33 (0.29), residues: 288 loop : -0.27 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 430 TYR 0.017 0.001 TYR B 236 PHE 0.014 0.001 PHE D 57 TRP 0.009 0.001 TRP D 183 HIS 0.004 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00323 (17036) covalent geometry : angle 0.52982 (23240) hydrogen bonds : bond 0.03652 ( 672) hydrogen bonds : angle 5.36897 ( 1860) Misc. bond : bond 0.01781 ( 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 176 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.660 Fit side-chains REVERT: A 240 GLN cc_start: 0.8221 (mp-120) cc_final: 0.7666 (mp10) REVERT: B 240 GLN cc_start: 0.8213 (mp-120) cc_final: 0.7666 (mp10) REVERT: C 240 GLN cc_start: 0.8231 (mp-120) cc_final: 0.7675 (mp10) REVERT: C 350 MET cc_start: 0.8476 (mmm) cc_final: 0.8115 (mtp) REVERT: D 240 GLN cc_start: 0.8227 (mp-120) cc_final: 0.7675 (mp10) REVERT: D 350 MET cc_start: 0.8458 (mmm) cc_final: 0.8101 (mtp) outliers start: 33 outliers final: 16 residues processed: 156 average time/residue: 0.1065 time to fit residues: 26.5238 Evaluate side-chains 154 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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 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 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 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 172 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.111593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.098530 restraints weight = 21752.353| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 0.94 r_work: 0.2911 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17040 Z= 0.183 Angle : 0.583 6.421 23240 Z= 0.291 Chirality : 0.045 0.150 2348 Planarity : 0.005 0.053 3080 Dihedral : 7.086 73.041 2272 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.74 % Allowed : 10.59 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.18), residues: 2000 helix: 1.36 (0.20), residues: 700 sheet: 0.21 (0.29), residues: 288 loop : -0.33 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 430 TYR 0.020 0.002 TYR B 236 PHE 0.013 0.002 PHE C 57 TRP 0.009 0.001 TRP D 183 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00464 (17036) covalent geometry : angle 0.58341 (23240) hydrogen bonds : bond 0.04121 ( 672) hydrogen bonds : angle 5.52340 ( 1860) Misc. bond : bond 0.04891 ( 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 174 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.521 Fit side-chains REVERT: A 240 GLN cc_start: 0.8310 (mp-120) cc_final: 0.7785 (mp10) REVERT: B 240 GLN cc_start: 0.8312 (mp-120) cc_final: 0.7790 (mp10) REVERT: C 240 GLN cc_start: 0.8327 (mp-120) cc_final: 0.7792 (mp10) REVERT: D 240 GLN cc_start: 0.8321 (mp-120) cc_final: 0.7790 (mp10) outliers start: 30 outliers final: 16 residues processed: 156 average time/residue: 0.1185 time to fit residues: 28.6738 Evaluate side-chains 154 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 185 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3212 r_free = 0.3212 target = 0.113301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.100421 restraints weight = 21516.395| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 0.92 r_work: 0.2942 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3533 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= 0.132 Angle : 0.540 7.293 23240 Z= 0.267 Chirality : 0.043 0.152 2348 Planarity : 0.005 0.053 3080 Dihedral : 6.927 71.258 2272 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.27 % Allowed : 11.23 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.18), residues: 2000 helix: 1.50 (0.20), residues: 696 sheet: 0.30 (0.29), residues: 288 loop : -0.28 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 430 TYR 0.018 0.001 TYR A 236 PHE 0.022 0.001 PHE D 57 TRP 0.009 0.001 TRP A 183 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00331 (17036) covalent geometry : angle 0.54032 (23240) hydrogen bonds : bond 0.03767 ( 672) hydrogen bonds : angle 5.33796 ( 1860) Misc. bond : bond 0.02023 ( 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 165 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.546 Fit side-chains REVERT: A 240 GLN cc_start: 0.8201 (mp-120) cc_final: 0.7593 (mp10) REVERT: B 240 GLN cc_start: 0.8202 (mp-120) cc_final: 0.7589 (mp10) REVERT: C 61 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7677 (mtp) REVERT: C 240 GLN cc_start: 0.8206 (mp-120) cc_final: 0.7615 (mp10) REVERT: D 61 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7669 (mtp) REVERT: D 240 GLN cc_start: 0.8208 (mp-120) cc_final: 0.7622 (mp10) outliers start: 22 outliers final: 16 residues processed: 149 average time/residue: 0.1100 time to fit residues: 26.1793 Evaluate side-chains 151 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 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 C residue 18 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 5 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 157 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3218 r_free = 0.3218 target = 0.113807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.100742 restraints weight = 21524.700| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 0.93 r_work: 0.2946 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17040 Z= 0.121 Angle : 0.540 7.655 23240 Z= 0.267 Chirality : 0.043 0.151 2348 Planarity : 0.005 0.052 3080 Dihedral : 6.806 69.803 2272 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.33 % Allowed : 11.57 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.19), residues: 2000 helix: 1.61 (0.20), residues: 692 sheet: 0.30 (0.29), residues: 288 loop : -0.19 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 430 TYR 0.017 0.001 TYR B 236 PHE 0.019 0.001 PHE D 57 TRP 0.009 0.001 TRP C 183 HIS 0.004 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00301 (17036) covalent geometry : angle 0.54003 (23240) hydrogen bonds : bond 0.03658 ( 672) hydrogen bonds : angle 5.26176 ( 1860) Misc. bond : bond 0.01764 ( 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 176 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.640 Fit side-chains REVERT: A 240 GLN cc_start: 0.8193 (mp-120) cc_final: 0.7634 (mp10) REVERT: B 240 GLN cc_start: 0.8195 (mp-120) cc_final: 0.7628 (mp10) REVERT: C 61 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7699 (mtp) REVERT: C 240 GLN cc_start: 0.8199 (mp-120) cc_final: 0.7642 (mp10) REVERT: C 350 MET cc_start: 0.8445 (mmm) cc_final: 0.8193 (mmm) REVERT: C 425 TYR cc_start: 0.8489 (m-80) cc_final: 0.8284 (m-80) REVERT: D 61 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7732 (mtp) REVERT: D 240 GLN cc_start: 0.8201 (mp-120) cc_final: 0.7651 (mp10) REVERT: D 350 MET cc_start: 0.8466 (mmm) cc_final: 0.8219 (mmm) REVERT: D 425 TYR cc_start: 0.8485 (m-80) cc_final: 0.8270 (m-80) outliers start: 23 outliers final: 16 residues processed: 160 average time/residue: 0.1244 time to fit residues: 31.0466 Evaluate side-chains 156 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 C residue 18 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 154 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 178 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.115020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.102166 restraints weight = 21210.828| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 0.92 r_work: 0.2964 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3710 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= 0.107 Angle : 0.528 7.540 23240 Z= 0.260 Chirality : 0.042 0.151 2348 Planarity : 0.005 0.052 3080 Dihedral : 6.652 67.213 2272 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.04 % Allowed : 11.92 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.19), residues: 2000 helix: 1.64 (0.20), residues: 696 sheet: 0.43 (0.30), residues: 288 loop : -0.16 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 430 TYR 0.016 0.001 TYR D 236 PHE 0.029 0.001 PHE B 57 TRP 0.009 0.001 TRP B 183 HIS 0.004 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00264 (17036) covalent geometry : angle 0.52768 (23240) hydrogen bonds : bond 0.03455 ( 672) hydrogen bonds : angle 5.11599 ( 1860) Misc. bond : bond 0.01101 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3037.10 seconds wall clock time: 53 minutes 5.24 seconds (3185.24 seconds total)