Starting phenix.real_space_refine on Mon Nov 18 14:41:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvd_17962/11_2024/8pvd_17962.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvd_17962/11_2024/8pvd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvd_17962/11_2024/8pvd_17962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvd_17962/11_2024/8pvd_17962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvd_17962/11_2024/8pvd_17962.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvd_17962/11_2024/8pvd_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.84, per 1000 atoms: 0.54 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: 4.19 Conformation dependent library (CDL) restraints added in 2.0 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: 1.64 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: 5.59 Time building geometry restraints manager: 4.75 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: 0.00 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.240 Process input model: 36.360 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.030 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.690 ------------------------------------------------------------------------------- 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 17036 Z= 0.793 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 *********************** 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 : 2.023 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: 0.3661 time to fit residues: 175.4535 Evaluate side-chains 162 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 2.149 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 17036 Z= 0.185 Angle : 0.584 5.485 23240 Z= 0.300 Chirality : 0.044 0.156 2348 Planarity : 0.004 0.033 3080 Dihedral : 7.756 79.872 2272 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.20 % Favored : 97.60 % Rotamer: Outliers : 1.50 % Allowed : 8.68 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2000 helix: 1.15 (0.19), residues: 712 sheet: 0.49 (0.27), residues: 332 loop : -0.09 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 183 HIS 0.005 0.001 HIS D 235 PHE 0.009 0.001 PHE A 154 TYR 0.021 0.001 TYR B 236 ARG 0.004 0.001 ARG A 170 *********************** 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 : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.6881 (tt0) cc_final: 0.6629 (tp30) REVERT: A 212 MET cc_start: 0.8270 (ptt) cc_final: 0.8062 (ptt) REVERT: A 243 LYS cc_start: 0.7108 (ttpt) cc_final: 0.6477 (ttpt) REVERT: A 293 PRO cc_start: 0.7473 (Cg_exo) cc_final: 0.7240 (Cg_endo) REVERT: A 360 ASP cc_start: 0.8346 (t70) cc_final: 0.7905 (t0) REVERT: A 428 GLU cc_start: 0.6890 (mt-10) cc_final: 0.5983 (mp0) REVERT: A 453 GLU cc_start: 0.4276 (mm-30) cc_final: 0.3861 (mm-30) REVERT: A 457 LYS cc_start: 0.5760 (tttm) cc_final: 0.5435 (mptt) REVERT: A 461 GLU cc_start: 0.5873 (mt-10) cc_final: 0.5651 (mt-10) REVERT: B 60 GLU cc_start: 0.6877 (tt0) cc_final: 0.6629 (tp30) REVERT: B 212 MET cc_start: 0.8268 (ptt) cc_final: 0.8059 (ptt) REVERT: B 243 LYS cc_start: 0.7106 (ttpt) cc_final: 0.6473 (ttpt) REVERT: B 293 PRO cc_start: 0.7474 (Cg_exo) cc_final: 0.7242 (Cg_endo) REVERT: B 360 ASP cc_start: 0.8350 (t70) cc_final: 0.7909 (t0) REVERT: B 428 GLU cc_start: 0.6887 (mt-10) cc_final: 0.5982 (mp0) REVERT: B 453 GLU cc_start: 0.4272 (mm-30) cc_final: 0.3861 (mm-30) REVERT: B 457 LYS cc_start: 0.5762 (tttm) cc_final: 0.5435 (mptt) REVERT: B 461 GLU cc_start: 0.5869 (mt-10) cc_final: 0.5647 (mt-10) REVERT: C 60 GLU cc_start: 0.6876 (tt0) cc_final: 0.6627 (tp30) REVERT: C 212 MET cc_start: 0.8269 (ptt) cc_final: 0.8063 (ptt) REVERT: C 243 LYS cc_start: 0.7111 (ttpt) cc_final: 0.6478 (ttpt) REVERT: C 293 PRO cc_start: 0.7473 (Cg_exo) cc_final: 0.7240 (Cg_endo) REVERT: C 360 ASP cc_start: 0.8339 (t70) cc_final: 0.7899 (t0) REVERT: C 424 GLN cc_start: 0.7081 (tt0) cc_final: 0.6065 (mp10) REVERT: C 428 GLU cc_start: 0.6893 (mt-10) cc_final: 0.5996 (mp0) REVERT: C 453 GLU cc_start: 0.4274 (mm-30) cc_final: 0.3859 (mm-30) REVERT: C 457 LYS cc_start: 0.5758 (tttm) cc_final: 0.5433 (mptt) REVERT: C 461 GLU cc_start: 0.5870 (mt-10) cc_final: 0.5647 (mt-10) REVERT: D 60 GLU cc_start: 0.6879 (tt0) cc_final: 0.6630 (tp30) REVERT: D 212 MET cc_start: 0.8273 (ptt) cc_final: 0.8066 (ptt) REVERT: D 243 LYS cc_start: 0.7108 (ttpt) cc_final: 0.6477 (ttpt) REVERT: D 293 PRO cc_start: 0.7472 (Cg_exo) cc_final: 0.7239 (Cg_endo) REVERT: D 360 ASP cc_start: 0.8346 (t70) cc_final: 0.7906 (t0) REVERT: D 424 GLN cc_start: 0.7082 (tt0) cc_final: 0.6067 (mp10) REVERT: D 428 GLU cc_start: 0.6894 (mt-10) cc_final: 0.5998 (mp0) REVERT: D 453 GLU cc_start: 0.4270 (mm-30) cc_final: 0.3856 (mm-30) REVERT: D 457 LYS cc_start: 0.5762 (tttm) cc_final: 0.5436 (mptt) REVERT: D 461 GLU cc_start: 0.5873 (mt-10) cc_final: 0.5652 (mt-10) outliers start: 26 outliers final: 18 residues processed: 194 average time/residue: 0.2875 time to fit residues: 85.2662 Evaluate side-chains 174 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.994 ------------------------------------------------------------------------------- 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 100 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17036 Z= 0.260 Angle : 0.591 6.047 23240 Z= 0.293 Chirality : 0.045 0.154 2348 Planarity : 0.005 0.040 3080 Dihedral : 7.305 77.310 2272 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.35 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 (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: 0.70 (0.18), residues: 2000 helix: 1.34 (0.19), residues: 708 sheet: 0.68 (0.29), residues: 304 loop : -0.18 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.004 0.001 HIS C 235 PHE 0.013 0.002 PHE D 136 TYR 0.019 0.002 TYR B 236 ARG 0.003 0.000 ARG D 354 *********************** 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 188 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 2.023 Fit side-chains REVERT: A 157 ASP cc_start: 0.7613 (t70) cc_final: 0.7413 (t0) REVERT: A 212 MET cc_start: 0.8490 (ptt) cc_final: 0.8214 (ptt) REVERT: A 240 GLN cc_start: 0.7692 (mp-120) cc_final: 0.6817 (mp10) REVERT: A 360 ASP cc_start: 0.8236 (t70) cc_final: 0.7848 (t0) REVERT: A 428 GLU cc_start: 0.6876 (mt-10) cc_final: 0.5924 (mp0) REVERT: A 453 GLU cc_start: 0.4312 (mm-30) cc_final: 0.3890 (mm-30) REVERT: B 157 ASP cc_start: 0.7610 (t70) cc_final: 0.7407 (t0) REVERT: B 212 MET cc_start: 0.8491 (ptt) cc_final: 0.8214 (ptt) REVERT: B 240 GLN cc_start: 0.7698 (mp-120) cc_final: 0.6816 (mp10) REVERT: B 360 ASP cc_start: 0.8236 (t70) cc_final: 0.7850 (t0) REVERT: B 428 GLU cc_start: 0.6873 (mt-10) cc_final: 0.5922 (mp0) REVERT: B 453 GLU cc_start: 0.4310 (mm-30) cc_final: 0.3890 (mm-30) REVERT: C 157 ASP cc_start: 0.7611 (t70) cc_final: 0.7406 (t0) REVERT: C 212 MET cc_start: 0.8491 (ptt) cc_final: 0.8218 (ptt) REVERT: C 240 GLN cc_start: 0.7695 (mp-120) cc_final: 0.6815 (mp10) REVERT: C 360 ASP cc_start: 0.8231 (t70) cc_final: 0.7844 (t0) REVERT: C 424 GLN cc_start: 0.7157 (tt0) cc_final: 0.6936 (tt0) REVERT: C 428 GLU cc_start: 0.6806 (mt-10) cc_final: 0.5961 (mp0) REVERT: C 453 GLU cc_start: 0.4312 (mm-30) cc_final: 0.3889 (mm-30) REVERT: D 157 ASP cc_start: 0.7608 (t70) cc_final: 0.7406 (t0) REVERT: D 212 MET cc_start: 0.8491 (ptt) cc_final: 0.8216 (ptt) REVERT: D 240 GLN cc_start: 0.7699 (mp-120) cc_final: 0.6822 (mp10) REVERT: D 360 ASP cc_start: 0.8234 (t70) cc_final: 0.7849 (t0) REVERT: D 424 GLN cc_start: 0.7160 (tt0) cc_final: 0.6939 (tt0) REVERT: D 428 GLU cc_start: 0.6811 (mt-10) cc_final: 0.5963 (mp0) REVERT: D 453 GLU cc_start: 0.4312 (mm-30) cc_final: 0.3889 (mm-30) outliers start: 28 outliers final: 20 residues processed: 176 average time/residue: 0.2804 time to fit residues: 77.8664 Evaluate side-chains 166 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN C 255 GLN C 471 GLN D 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17036 Z= 0.337 Angle : 0.622 7.007 23240 Z= 0.307 Chirality : 0.046 0.152 2348 Planarity : 0.005 0.053 3080 Dihedral : 7.354 76.119 2272 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.85 % Allowed : 8.80 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2000 helix: 1.19 (0.19), residues: 708 sheet: 0.68 (0.30), residues: 284 loop : -0.35 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 183 HIS 0.004 0.001 HIS A 235 PHE 0.014 0.002 PHE C 294 TYR 0.021 0.002 TYR B 236 ARG 0.003 0.000 ARG A 72 *********************** 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 178 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 1.908 Fit side-chains REVERT: A 60 GLU cc_start: 0.6664 (tt0) cc_final: 0.6450 (tp30) REVERT: A 240 GLN cc_start: 0.7814 (mp-120) cc_final: 0.6983 (mp10) REVERT: A 360 ASP cc_start: 0.8253 (t70) cc_final: 0.7914 (t0) REVERT: A 428 GLU cc_start: 0.6909 (mt-10) cc_final: 0.5912 (mp0) REVERT: B 60 GLU cc_start: 0.6663 (tt0) cc_final: 0.6445 (tp30) REVERT: B 240 GLN cc_start: 0.7814 (mp-120) cc_final: 0.6982 (mp10) REVERT: B 360 ASP cc_start: 0.8253 (t70) cc_final: 0.7915 (t0) REVERT: B 428 GLU cc_start: 0.6910 (mt-10) cc_final: 0.5913 (mp0) REVERT: C 60 GLU cc_start: 0.6663 (tt0) cc_final: 0.6444 (tp30) REVERT: C 240 GLN cc_start: 0.7811 (mp-120) cc_final: 0.6980 (mp10) REVERT: C 360 ASP cc_start: 0.8248 (t70) cc_final: 0.7908 (t0) REVERT: C 424 GLN cc_start: 0.7114 (tt0) cc_final: 0.6758 (tt0) REVERT: C 428 GLU cc_start: 0.6873 (mt-10) cc_final: 0.5979 (mp0) REVERT: D 60 GLU cc_start: 0.6678 (tt0) cc_final: 0.6457 (tp30) REVERT: D 240 GLN cc_start: 0.7816 (mp-120) cc_final: 0.6985 (mp10) REVERT: D 360 ASP cc_start: 0.8254 (t70) cc_final: 0.7916 (t0) REVERT: D 424 GLN cc_start: 0.7117 (tt0) cc_final: 0.6760 (tt0) REVERT: D 428 GLU cc_start: 0.6883 (mt-10) cc_final: 0.5988 (mp0) outliers start: 32 outliers final: 16 residues processed: 162 average time/residue: 0.2663 time to fit residues: 68.5829 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 : 1.956 ------------------------------------------------------------------------------- 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 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 161 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 164 optimal weight: 0.1980 chunk 133 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN B 492 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN D 492 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17036 Z= 0.150 Angle : 0.517 6.107 23240 Z= 0.249 Chirality : 0.042 0.153 2348 Planarity : 0.004 0.050 3080 Dihedral : 6.850 70.934 2272 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.97 % Allowed : 9.84 % 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 (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: 0.80 (0.19), residues: 2000 helix: 1.50 (0.19), residues: 724 sheet: 0.67 (0.30), residues: 288 loop : -0.19 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 183 HIS 0.003 0.000 HIS D 235 PHE 0.009 0.001 PHE D 136 TYR 0.014 0.001 TYR A 236 ARG 0.002 0.000 ARG D 72 *********************** 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 218 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.6037 (p0) cc_final: 0.5792 (p0) REVERT: A 122 SER cc_start: 0.7880 (t) cc_final: 0.7564 (m) REVERT: A 212 MET cc_start: 0.8453 (ptt) cc_final: 0.8211 (ptt) REVERT: A 360 ASP cc_start: 0.8129 (t70) cc_final: 0.7245 (t0) REVERT: A 428 GLU cc_start: 0.6819 (mt-10) cc_final: 0.5793 (mp0) REVERT: B 6 ASP cc_start: 0.6045 (p0) cc_final: 0.5798 (p0) REVERT: B 122 SER cc_start: 0.7879 (t) cc_final: 0.7564 (m) REVERT: B 212 MET cc_start: 0.8455 (ptt) cc_final: 0.8210 (ptt) REVERT: B 360 ASP cc_start: 0.8133 (t70) cc_final: 0.7244 (t0) REVERT: B 428 GLU cc_start: 0.6817 (mt-10) cc_final: 0.5793 (mp0) REVERT: C 6 ASP cc_start: 0.6048 (p0) cc_final: 0.5802 (p0) REVERT: C 122 SER cc_start: 0.7890 (OUTLIER) cc_final: 0.7564 (m) REVERT: C 212 MET cc_start: 0.8452 (ptt) cc_final: 0.8209 (ptt) REVERT: C 360 ASP cc_start: 0.8126 (t70) cc_final: 0.7237 (t0) REVERT: C 424 GLN cc_start: 0.7175 (tt0) cc_final: 0.6796 (tt0) REVERT: C 428 GLU cc_start: 0.6782 (mt-10) cc_final: 0.5873 (mp0) REVERT: D 6 ASP cc_start: 0.6044 (p0) cc_final: 0.5797 (p0) REVERT: D 122 SER cc_start: 0.7889 (OUTLIER) cc_final: 0.7563 (m) REVERT: D 212 MET cc_start: 0.8461 (ptt) cc_final: 0.8217 (ptt) REVERT: D 360 ASP cc_start: 0.8129 (t70) cc_final: 0.7240 (t0) REVERT: D 424 GLN cc_start: 0.7174 (tt0) cc_final: 0.6796 (tt0) REVERT: D 428 GLU cc_start: 0.6792 (mt-10) cc_final: 0.5881 (mp0) outliers start: 34 outliers final: 20 residues processed: 200 average time/residue: 0.2664 time to fit residues: 83.7258 Evaluate side-chains 186 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 52 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 255 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17036 Z= 0.182 Angle : 0.529 6.413 23240 Z= 0.260 Chirality : 0.043 0.152 2348 Planarity : 0.004 0.047 3080 Dihedral : 6.858 70.095 2272 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: 0.86 (0.19), residues: 2000 helix: 1.64 (0.19), residues: 716 sheet: 0.66 (0.30), residues: 288 loop : -0.20 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 183 HIS 0.004 0.001 HIS B 235 PHE 0.012 0.001 PHE D 57 TYR 0.016 0.001 TYR A 236 ARG 0.004 0.000 ARG B 354 *********************** 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 189 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.932 Fit side-chains REVERT: A 122 SER cc_start: 0.7898 (t) cc_final: 0.7594 (m) REVERT: A 212 MET cc_start: 0.8472 (ptt) cc_final: 0.8234 (ptt) REVERT: A 240 GLN cc_start: 0.7747 (mp-120) cc_final: 0.6813 (mp10) REVERT: A 360 ASP cc_start: 0.8128 (t70) cc_final: 0.7699 (t0) REVERT: A 428 GLU cc_start: 0.6818 (mt-10) cc_final: 0.5781 (mp0) REVERT: B 122 SER cc_start: 0.7894 (t) cc_final: 0.7592 (m) REVERT: B 212 MET cc_start: 0.8474 (ptt) cc_final: 0.8236 (ptt) REVERT: B 240 GLN cc_start: 0.7755 (mp-120) cc_final: 0.6814 (mp10) REVERT: B 360 ASP cc_start: 0.8127 (t70) cc_final: 0.7695 (t0) REVERT: B 428 GLU cc_start: 0.6814 (mt-10) cc_final: 0.5780 (mp0) REVERT: C 122 SER cc_start: 0.7904 (t) cc_final: 0.7604 (m) REVERT: C 212 MET cc_start: 0.8470 (ptt) cc_final: 0.8231 (ptt) REVERT: C 240 GLN cc_start: 0.7750 (mp-120) cc_final: 0.6812 (mp10) REVERT: C 360 ASP cc_start: 0.8123 (t70) cc_final: 0.7674 (t0) REVERT: C 424 GLN cc_start: 0.7148 (tt0) cc_final: 0.6751 (tt0) REVERT: C 428 GLU cc_start: 0.6787 (mt-10) cc_final: 0.5875 (mp0) REVERT: D 6 ASP cc_start: 0.6059 (p0) cc_final: 0.5775 (p0) REVERT: D 122 SER cc_start: 0.7907 (t) cc_final: 0.7608 (m) REVERT: D 212 MET cc_start: 0.8477 (ptt) cc_final: 0.8236 (ptt) REVERT: D 240 GLN cc_start: 0.7755 (mp-120) cc_final: 0.6818 (mp10) REVERT: D 360 ASP cc_start: 0.8127 (t70) cc_final: 0.7678 (t0) REVERT: D 424 GLN cc_start: 0.7146 (tt0) cc_final: 0.6748 (tt0) REVERT: D 428 GLU cc_start: 0.6800 (mt-10) cc_final: 0.5886 (mp0) outliers start: 24 outliers final: 24 residues processed: 169 average time/residue: 0.2741 time to fit residues: 72.7097 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 : 2.028 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17036 Z= 0.242 Angle : 0.556 7.404 23240 Z= 0.275 Chirality : 0.044 0.150 2348 Planarity : 0.004 0.047 3080 Dihedral : 6.941 70.940 2272 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.85 % Allowed : 10.88 % Favored : 87.27 % 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: 0.63 (0.19), residues: 2000 helix: 1.46 (0.19), residues: 716 sheet: 0.41 (0.30), residues: 288 loop : -0.30 (0.19), residues: 996 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 0.012 0.001 PHE B 57 TYR 0.018 0.002 TYR B 236 ARG 0.005 0.000 ARG B 354 *********************** 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 194 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 1.879 Fit side-chains REVERT: A 122 SER cc_start: 0.7986 (t) cc_final: 0.7689 (m) REVERT: A 240 GLN cc_start: 0.7737 (mp-120) cc_final: 0.6769 (mp10) REVERT: A 360 ASP cc_start: 0.8126 (t70) cc_final: 0.7682 (t0) REVERT: A 428 GLU cc_start: 0.6870 (mt-10) cc_final: 0.5920 (mp0) REVERT: A 458 ARG cc_start: 0.5620 (mtm-85) cc_final: 0.5280 (ttm-80) REVERT: B 122 SER cc_start: 0.7986 (t) cc_final: 0.7691 (m) REVERT: B 240 GLN cc_start: 0.7744 (mp-120) cc_final: 0.6770 (mp10) REVERT: B 360 ASP cc_start: 0.8125 (t70) cc_final: 0.7678 (t0) REVERT: B 428 GLU cc_start: 0.6870 (mt-10) cc_final: 0.5922 (mp0) REVERT: B 458 ARG cc_start: 0.5669 (mtm-85) cc_final: 0.5324 (ttm-80) REVERT: C 61 MET cc_start: 0.6866 (tpp) cc_final: 0.6654 (tpp) REVERT: C 122 SER cc_start: 0.8006 (t) cc_final: 0.7707 (m) REVERT: C 240 GLN cc_start: 0.7740 (mp-120) cc_final: 0.6769 (mp10) REVERT: C 257 ASP cc_start: 0.6702 (t0) cc_final: 0.6077 (p0) REVERT: C 360 ASP cc_start: 0.8093 (t70) cc_final: 0.7655 (t0) REVERT: C 424 GLN cc_start: 0.7038 (tt0) cc_final: 0.6768 (tt0) REVERT: C 428 GLU cc_start: 0.6802 (mt-10) cc_final: 0.5881 (mp0) REVERT: C 458 ARG cc_start: 0.5672 (mtm-85) cc_final: 0.5326 (ttm-80) REVERT: D 122 SER cc_start: 0.8009 (t) cc_final: 0.7710 (m) REVERT: D 240 GLN cc_start: 0.7744 (mp-120) cc_final: 0.6775 (mp10) REVERT: D 257 ASP cc_start: 0.6708 (t0) cc_final: 0.6077 (p0) REVERT: D 360 ASP cc_start: 0.8098 (t70) cc_final: 0.7658 (t0) REVERT: D 424 GLN cc_start: 0.7037 (tt0) cc_final: 0.6767 (tt0) REVERT: D 428 GLU cc_start: 0.6817 (mt-10) cc_final: 0.5893 (mp0) REVERT: D 458 ARG cc_start: 0.5678 (mtm-85) cc_final: 0.5330 (ttm-80) outliers start: 32 outliers final: 24 residues processed: 174 average time/residue: 0.3147 time to fit residues: 85.1891 Evaluate side-chains 182 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 128 ASP 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 51 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17036 Z= 0.166 Angle : 0.525 7.254 23240 Z= 0.256 Chirality : 0.042 0.152 2348 Planarity : 0.004 0.049 3080 Dihedral : 6.711 67.638 2272 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.62 % Allowed : 11.28 % 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 (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: 0.79 (0.19), residues: 2000 helix: 1.58 (0.19), residues: 716 sheet: 0.57 (0.30), residues: 288 loop : -0.21 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.004 0.001 HIS D 235 PHE 0.015 0.001 PHE D 57 TYR 0.015 0.001 TYR B 236 ARG 0.004 0.000 ARG A 354 *********************** 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 202 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 1.842 Fit side-chains REVERT: A 6 ASP cc_start: 0.6079 (p0) cc_final: 0.5861 (p0) REVERT: A 122 SER cc_start: 0.7926 (t) cc_final: 0.7631 (m) REVERT: A 212 MET cc_start: 0.8547 (ptt) cc_final: 0.8311 (ptt) REVERT: A 240 GLN cc_start: 0.7726 (mp-120) cc_final: 0.6778 (mp10) REVERT: A 356 PHE cc_start: 0.7378 (t80) cc_final: 0.7152 (t80) REVERT: A 360 ASP cc_start: 0.8081 (t70) cc_final: 0.7629 (t0) REVERT: A 425 TYR cc_start: 0.7725 (m-80) cc_final: 0.7470 (m-80) REVERT: A 428 GLU cc_start: 0.6753 (mt-10) cc_final: 0.5831 (mp0) REVERT: A 458 ARG cc_start: 0.5641 (mtm-85) cc_final: 0.5304 (ttm-80) REVERT: B 6 ASP cc_start: 0.6089 (p0) cc_final: 0.5868 (p0) REVERT: B 122 SER cc_start: 0.7922 (t) cc_final: 0.7629 (m) REVERT: B 212 MET cc_start: 0.8550 (ptt) cc_final: 0.8312 (ptt) REVERT: B 240 GLN cc_start: 0.7733 (mp-120) cc_final: 0.6781 (mp10) REVERT: B 360 ASP cc_start: 0.8092 (t70) cc_final: 0.7652 (t0) REVERT: B 425 TYR cc_start: 0.7729 (m-80) cc_final: 0.7478 (m-80) REVERT: B 428 GLU cc_start: 0.6751 (mt-10) cc_final: 0.5832 (mp0) REVERT: B 458 ARG cc_start: 0.5639 (mtm-85) cc_final: 0.5302 (ttm-80) REVERT: C 61 MET cc_start: 0.6771 (tpp) cc_final: 0.6431 (tpp) REVERT: C 122 SER cc_start: 0.7915 (t) cc_final: 0.7620 (m) REVERT: C 240 GLN cc_start: 0.7729 (mp-120) cc_final: 0.6773 (mp10) REVERT: C 257 ASP cc_start: 0.6703 (t0) cc_final: 0.6072 (p0) REVERT: C 356 PHE cc_start: 0.7369 (t80) cc_final: 0.7138 (t80) REVERT: C 360 ASP cc_start: 0.8078 (t70) cc_final: 0.7648 (t0) REVERT: C 424 GLN cc_start: 0.7055 (tt0) cc_final: 0.6746 (tt0) REVERT: C 425 TYR cc_start: 0.7724 (m-80) cc_final: 0.7464 (m-80) REVERT: C 428 GLU cc_start: 0.6767 (mt-10) cc_final: 0.5852 (mp0) REVERT: C 458 ARG cc_start: 0.5640 (mtm-85) cc_final: 0.5305 (ttm-80) REVERT: D 122 SER cc_start: 0.7917 (t) cc_final: 0.7622 (m) REVERT: D 240 GLN cc_start: 0.7732 (mp-120) cc_final: 0.6777 (mp10) REVERT: D 257 ASP cc_start: 0.6708 (t0) cc_final: 0.6071 (p0) REVERT: D 356 PHE cc_start: 0.7368 (t80) cc_final: 0.7143 (t80) REVERT: D 360 ASP cc_start: 0.8081 (t70) cc_final: 0.7648 (t0) REVERT: D 424 GLN cc_start: 0.7052 (tt0) cc_final: 0.6744 (tt0) REVERT: D 425 TYR cc_start: 0.7721 (m-80) cc_final: 0.7464 (m-80) REVERT: D 428 GLU cc_start: 0.6779 (mt-10) cc_final: 0.5863 (mp0) outliers start: 28 outliers final: 24 residues processed: 182 average time/residue: 0.2813 time to fit residues: 79.3915 Evaluate side-chains 182 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17036 Z= 0.281 Angle : 0.584 7.821 23240 Z= 0.286 Chirality : 0.045 0.148 2348 Planarity : 0.005 0.049 3080 Dihedral : 6.950 70.669 2272 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.91 % Allowed : 11.23 % Favored : 86.86 % 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: 0.55 (0.18), residues: 2000 helix: 1.42 (0.19), residues: 712 sheet: 0.40 (0.29), residues: 288 loop : -0.38 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 183 HIS 0.004 0.001 HIS C 235 PHE 0.018 0.002 PHE D 57 TYR 0.019 0.002 TYR C 236 ARG 0.005 0.000 ARG B 354 *********************** 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 189 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 2.171 Fit side-chains REVERT: A 122 SER cc_start: 0.7916 (t) cc_final: 0.7627 (m) REVERT: A 240 GLN cc_start: 0.7845 (mp-120) cc_final: 0.6877 (mp10) REVERT: A 257 ASP cc_start: 0.6955 (t0) cc_final: 0.6126 (p0) REVERT: A 356 PHE cc_start: 0.7389 (t80) cc_final: 0.7103 (t80) REVERT: A 360 ASP cc_start: 0.8091 (t70) cc_final: 0.7640 (t0) REVERT: A 425 TYR cc_start: 0.7747 (m-80) cc_final: 0.7445 (m-80) REVERT: A 428 GLU cc_start: 0.6903 (mt-10) cc_final: 0.5916 (mp0) REVERT: B 122 SER cc_start: 0.7914 (t) cc_final: 0.7628 (m) REVERT: B 240 GLN cc_start: 0.7850 (mp-120) cc_final: 0.6880 (mp10) REVERT: B 257 ASP cc_start: 0.6956 (t0) cc_final: 0.6125 (p0) REVERT: B 356 PHE cc_start: 0.7404 (t80) cc_final: 0.7109 (t80) REVERT: B 360 ASP cc_start: 0.8132 (t70) cc_final: 0.7677 (t0) REVERT: B 425 TYR cc_start: 0.7755 (m-80) cc_final: 0.7459 (m-80) REVERT: B 428 GLU cc_start: 0.6906 (mt-10) cc_final: 0.5918 (mp0) REVERT: C 61 MET cc_start: 0.6844 (tpp) cc_final: 0.6550 (tpp) REVERT: C 122 SER cc_start: 0.7923 (t) cc_final: 0.7622 (m) REVERT: C 240 GLN cc_start: 0.7847 (mp-120) cc_final: 0.6875 (mp10) REVERT: C 257 ASP cc_start: 0.6722 (t0) cc_final: 0.6083 (p0) REVERT: C 356 PHE cc_start: 0.7411 (t80) cc_final: 0.7114 (t80) REVERT: C 360 ASP cc_start: 0.8114 (t70) cc_final: 0.7669 (t0) REVERT: C 424 GLN cc_start: 0.7027 (tt0) cc_final: 0.6669 (tt0) REVERT: C 425 TYR cc_start: 0.7683 (m-80) cc_final: 0.7379 (m-80) REVERT: C 428 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6045 (mp0) REVERT: D 61 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6681 (mtp) REVERT: D 122 SER cc_start: 0.7924 (t) cc_final: 0.7625 (m) REVERT: D 240 GLN cc_start: 0.7849 (mp-120) cc_final: 0.6881 (mp10) REVERT: D 257 ASP cc_start: 0.6727 (t0) cc_final: 0.6081 (p0) REVERT: D 356 PHE cc_start: 0.7395 (t80) cc_final: 0.7094 (t80) REVERT: D 360 ASP cc_start: 0.8116 (t70) cc_final: 0.7668 (t0) REVERT: D 424 GLN cc_start: 0.7029 (tt0) cc_final: 0.6673 (tt0) REVERT: D 425 TYR cc_start: 0.7681 (m-80) cc_final: 0.7380 (m-80) REVERT: D 428 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6054 (mp0) outliers start: 33 outliers final: 20 residues processed: 168 average time/residue: 0.2873 time to fit residues: 76.3517 Evaluate side-chains 175 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 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 115 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 122 optimal weight: 0.2980 chunk 97 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17036 Z= 0.164 Angle : 0.526 7.280 23240 Z= 0.258 Chirality : 0.042 0.153 2348 Planarity : 0.004 0.050 3080 Dihedral : 6.672 66.757 2272 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.39 % Allowed : 11.63 % Favored : 86.98 % 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: 0.75 (0.19), residues: 2000 helix: 1.48 (0.19), residues: 720 sheet: 0.57 (0.30), residues: 288 loop : -0.19 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 183 HIS 0.004 0.001 HIS B 235 PHE 0.018 0.001 PHE D 57 TYR 0.015 0.001 TYR D 236 ARG 0.003 0.000 ARG B 354 ********************** 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 196 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.6197 (t0) cc_final: 0.5439 (p0) REVERT: A 122 SER cc_start: 0.7943 (t) cc_final: 0.7655 (m) REVERT: A 212 MET cc_start: 0.8543 (ptt) cc_final: 0.8292 (ptt) REVERT: A 257 ASP cc_start: 0.6850 (t0) cc_final: 0.6113 (p0) REVERT: A 356 PHE cc_start: 0.7368 (t80) cc_final: 0.7153 (t80) REVERT: A 360 ASP cc_start: 0.8073 (t70) cc_final: 0.7645 (t0) REVERT: A 425 TYR cc_start: 0.7692 (m-80) cc_final: 0.7385 (m-80) REVERT: A 428 GLU cc_start: 0.6673 (mt-10) cc_final: 0.5738 (mp0) REVERT: A 458 ARG cc_start: 0.5650 (mtm-85) cc_final: 0.5311 (ttm-80) REVERT: B 54 ASP cc_start: 0.6202 (t0) cc_final: 0.5446 (p0) REVERT: B 122 SER cc_start: 0.7935 (t) cc_final: 0.7650 (m) REVERT: B 212 MET cc_start: 0.8545 (ptt) cc_final: 0.8291 (ptt) REVERT: B 257 ASP cc_start: 0.6850 (t0) cc_final: 0.6113 (p0) REVERT: B 356 PHE cc_start: 0.7376 (t80) cc_final: 0.7140 (t80) REVERT: B 360 ASP cc_start: 0.8120 (t70) cc_final: 0.7688 (t0) REVERT: B 425 TYR cc_start: 0.7699 (m-80) cc_final: 0.7385 (m-80) REVERT: B 428 GLU cc_start: 0.6677 (mt-10) cc_final: 0.5741 (mp0) REVERT: B 458 ARG cc_start: 0.5648 (mtm-85) cc_final: 0.5308 (ttm-80) REVERT: C 61 MET cc_start: 0.6753 (tpp) cc_final: 0.6263 (tpp) REVERT: C 122 SER cc_start: 0.7944 (t) cc_final: 0.7654 (m) REVERT: C 257 ASP cc_start: 0.6677 (t0) cc_final: 0.6085 (p0) REVERT: C 356 PHE cc_start: 0.7387 (t80) cc_final: 0.7128 (t80) REVERT: C 360 ASP cc_start: 0.8094 (t70) cc_final: 0.7673 (t0) REVERT: C 424 GLN cc_start: 0.7021 (tt0) cc_final: 0.6691 (tt0) REVERT: C 425 TYR cc_start: 0.7639 (m-80) cc_final: 0.7304 (m-80) REVERT: C 428 GLU cc_start: 0.6753 (mt-10) cc_final: 0.5836 (mp0) REVERT: D 54 ASP cc_start: 0.6136 (t0) cc_final: 0.5373 (p0) REVERT: D 61 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6562 (mtp) REVERT: D 122 SER cc_start: 0.7945 (t) cc_final: 0.7658 (m) REVERT: D 257 ASP cc_start: 0.6680 (t0) cc_final: 0.6082 (p0) REVERT: D 356 PHE cc_start: 0.7382 (t80) cc_final: 0.7122 (t80) REVERT: D 360 ASP cc_start: 0.8077 (t70) cc_final: 0.7651 (t0) REVERT: D 424 GLN cc_start: 0.7021 (tt0) cc_final: 0.6699 (tt0) REVERT: D 425 TYR cc_start: 0.7635 (m-80) cc_final: 0.7308 (m-80) REVERT: D 428 GLU cc_start: 0.6766 (mt-10) cc_final: 0.5845 (mp0) REVERT: D 458 ARG cc_start: 0.5659 (mtm-85) cc_final: 0.5314 (ttm-80) outliers start: 24 outliers final: 19 residues processed: 176 average time/residue: 0.2841 time to fit residues: 77.6993 Evaluate side-chains 175 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 2.051 ------------------------------------------------------------------------------- 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 180 ASP 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 180 ASP 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 180 ASP 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 48 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 139 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 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 = 0.3260 r_free = 0.3260 target = 0.116813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103367 restraints weight = 21250.855| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 0.96 r_work: 0.2981 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17036 Z= 0.173 Angle : 0.528 7.404 23240 Z= 0.257 Chirality : 0.042 0.150 2348 Planarity : 0.004 0.049 3080 Dihedral : 6.605 64.087 2272 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.68 % Allowed : 11.34 % Favored : 86.98 % 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: 0.79 (0.19), residues: 2000 helix: 1.54 (0.19), residues: 716 sheet: 0.64 (0.30), residues: 288 loop : -0.20 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 183 HIS 0.004 0.001 HIS C 235 PHE 0.017 0.001 PHE D 57 TYR 0.016 0.001 TYR B 236 ARG 0.004 0.000 ARG B 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3189.78 seconds wall clock time: 59 minutes 23.80 seconds (3563.80 seconds total)