Starting phenix.real_space_refine on Sun Mar 17 15:50:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru0_24692/03_2024/7ru0_24692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru0_24692/03_2024/7ru0_24692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru0_24692/03_2024/7ru0_24692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru0_24692/03_2024/7ru0_24692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru0_24692/03_2024/7ru0_24692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru0_24692/03_2024/7ru0_24692_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6008 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 28 5.16 5 C 8044 2.51 5 N 2040 2.21 5 O 2168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 251": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "D GLU 251": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12284 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3049 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 2 Chain: "B" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3049 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 2 Chain: "C" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3049 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 2 Chain: "D" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3049 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 2 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 6.79, per 1000 atoms: 0.55 Number of scatterers: 12284 At special positions: 0 Unit cell: (111.282, 110.191, 113.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 4 15.00 O 2168 8.00 N 2040 7.00 C 8044 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 - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 4.99 Conformation dependent library (CDL) restraints added in 2.2 seconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 8 sheets defined 51.8% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 12 through 35 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.568A pdb=" N ALA A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 102 through 121 removed outlier: 4.256A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 113 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A 114 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 166 through 181 Processing helix chain 'A' and resid 194 through 222 Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.502A pdb=" N GLU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 No H-bonds generated for 'chain 'A' and resid 250 through 253' Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 273 through 276 No H-bonds generated for 'chain 'A' and resid 273 through 276' Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.658A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 removed outlier: 4.029A pdb=" N LEU A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 35 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 55 removed outlier: 3.568A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 102 through 121 removed outlier: 4.256A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU B 107 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 113 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS B 114 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 166 through 181 Processing helix chain 'B' and resid 194 through 222 Processing helix chain 'B' and resid 227 through 245 removed outlier: 3.502A pdb=" N GLU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 253 No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 257 through 265 Processing helix chain 'B' and resid 273 through 276 No H-bonds generated for 'chain 'B' and resid 273 through 276' Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.658A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 removed outlier: 4.029A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 35 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 44 through 55 removed outlier: 3.569A pdb=" N ALA C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 102 through 121 removed outlier: 4.256A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU C 107 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 113 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS C 114 " --> pdb=" O ARG C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 157 Processing helix chain 'C' and resid 166 through 181 Processing helix chain 'C' and resid 194 through 222 Processing helix chain 'C' and resid 227 through 245 removed outlier: 3.502A pdb=" N GLU C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 No H-bonds generated for 'chain 'C' and resid 250 through 253' Processing helix chain 'C' and resid 257 through 265 Processing helix chain 'C' and resid 273 through 276 No H-bonds generated for 'chain 'C' and resid 273 through 276' Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 308 through 313 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.658A pdb=" N SER C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 416 removed outlier: 4.028A pdb=" N LEU C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 35 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 44 through 55 removed outlier: 3.568A pdb=" N ALA D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 102 through 121 removed outlier: 4.256A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU D 107 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 113 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS D 114 " --> pdb=" O ARG D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 157 Processing helix chain 'D' and resid 166 through 181 Processing helix chain 'D' and resid 194 through 222 Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.502A pdb=" N GLU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 253 No H-bonds generated for 'chain 'D' and resid 250 through 253' Processing helix chain 'D' and resid 257 through 265 Processing helix chain 'D' and resid 273 through 276 No H-bonds generated for 'chain 'D' and resid 273 through 276' Processing helix chain 'D' and resid 281 through 291 Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.658A pdb=" N SER D 402 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 416 removed outlier: 4.029A pdb=" N LEU D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 319 through 322 removed outlier: 4.541A pdb=" N ASP A 388 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG A 343 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TYR A 390 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 341 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 346 through 348 Processing sheet with id= C, first strand: chain 'B' and resid 319 through 322 removed outlier: 4.541A pdb=" N ASP B 388 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG B 343 " --> pdb=" O ASP B 388 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TYR B 390 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE B 341 " --> pdb=" O TYR B 390 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 346 through 348 Processing sheet with id= E, first strand: chain 'C' and resid 319 through 322 removed outlier: 4.541A pdb=" N ASP C 388 " --> pdb=" O ARG C 343 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG C 343 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TYR C 390 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE C 341 " --> pdb=" O TYR C 390 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 346 through 348 Processing sheet with id= G, first strand: chain 'D' and resid 319 through 322 removed outlier: 4.541A pdb=" N ASP D 388 " --> pdb=" O ARG D 343 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG D 343 " --> pdb=" O ASP D 388 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TYR D 390 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE D 341 " --> pdb=" O TYR D 390 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 346 through 348 532 hydrogen bonds defined for protein. 1428 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: 3.07 Time building geometry restraints manager: 5.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3718 1.34 - 1.46: 1954 1.46 - 1.57: 6840 1.57 - 1.69: 8 1.69 - 1.81: 48 Bond restraints: 12568 Sorted by residual: bond pdb=" C SER B 157 " pdb=" N LEU B 158 " ideal model delta sigma weight residual 1.332 1.223 0.109 1.31e-02 5.83e+03 6.91e+01 bond pdb=" C SER A 157 " pdb=" N LEU A 158 " ideal model delta sigma weight residual 1.332 1.223 0.109 1.31e-02 5.83e+03 6.86e+01 bond pdb=" C SER D 157 " pdb=" N LEU D 158 " ideal model delta sigma weight residual 1.332 1.223 0.108 1.31e-02 5.83e+03 6.83e+01 bond pdb=" C SER C 157 " pdb=" N LEU C 158 " ideal model delta sigma weight residual 1.332 1.224 0.108 1.31e-02 5.83e+03 6.78e+01 bond pdb=" C LEU C 283 " pdb=" N ARG C 284 " ideal model delta sigma weight residual 1.335 1.243 0.092 1.38e-02 5.25e+03 4.44e+01 ... (remaining 12563 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.96: 480 106.96 - 114.31: 7251 114.31 - 121.65: 6782 121.65 - 129.00: 2523 129.00 - 136.34: 104 Bond angle restraints: 17140 Sorted by residual: angle pdb=" O SER C 157 " pdb=" C SER C 157 " pdb=" N LEU C 158 " ideal model delta sigma weight residual 122.07 115.71 6.36 1.03e+00 9.43e-01 3.82e+01 angle pdb=" O SER B 157 " pdb=" C SER B 157 " pdb=" N LEU B 158 " ideal model delta sigma weight residual 122.07 115.71 6.36 1.03e+00 9.43e-01 3.82e+01 angle pdb=" O SER A 157 " pdb=" C SER A 157 " pdb=" N LEU A 158 " ideal model delta sigma weight residual 122.07 115.71 6.36 1.03e+00 9.43e-01 3.81e+01 angle pdb=" O SER D 157 " pdb=" C SER D 157 " pdb=" N LEU D 158 " ideal model delta sigma weight residual 122.07 115.71 6.36 1.03e+00 9.43e-01 3.81e+01 angle pdb=" N ARG B 284 " pdb=" CA ARG B 284 " pdb=" C ARG B 284 " ideal model delta sigma weight residual 111.82 105.17 6.65 1.16e+00 7.43e-01 3.29e+01 ... (remaining 17135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.68: 7308 28.68 - 57.36: 208 57.36 - 86.03: 28 86.03 - 114.71: 0 114.71 - 143.39: 8 Dihedral angle restraints: 7552 sinusoidal: 3044 harmonic: 4508 Sorted by residual: dihedral pdb=" C5' CMP C 501 " pdb=" O5' CMP C 501 " pdb=" P CMP C 501 " pdb=" O1P CMP C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -179.61 -120.39 1 2.00e+01 2.50e-03 3.61e+01 dihedral pdb=" C5' CMP D 501 " pdb=" O5' CMP D 501 " pdb=" P CMP D 501 " pdb=" O1P CMP D 501 " ideal model delta sinusoidal sigma weight residual 60.00 -179.63 -120.37 1 2.00e+01 2.50e-03 3.61e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 -179.63 -120.37 1 2.00e+01 2.50e-03 3.61e+01 ... (remaining 7549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1496 0.059 - 0.118: 448 0.118 - 0.177: 101 0.177 - 0.236: 3 0.236 - 0.295: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA LYS D 298 " pdb=" N LYS D 298 " pdb=" C LYS D 298 " pdb=" CB LYS D 298 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LYS B 298 " pdb=" N LYS B 298 " pdb=" C LYS B 298 " pdb=" CB LYS B 298 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA LYS C 298 " pdb=" N LYS C 298 " pdb=" C LYS C 298 " pdb=" CB LYS C 298 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2049 not shown) Planarity restraints: 2100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 232 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C HIS A 232 " -0.055 2.00e-02 2.50e+03 pdb=" O HIS A 232 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 233 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 232 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C HIS C 232 " 0.055 2.00e-02 2.50e+03 pdb=" O HIS C 232 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG C 233 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 232 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.93e+00 pdb=" C HIS D 232 " 0.055 2.00e-02 2.50e+03 pdb=" O HIS D 232 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG D 233 " -0.018 2.00e-02 2.50e+03 ... (remaining 2097 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 406 2.70 - 3.25: 12438 3.25 - 3.80: 19364 3.80 - 4.35: 24081 4.35 - 4.90: 37992 Nonbonded interactions: 94281 Sorted by model distance: nonbonded pdb=" O LEU B 158 " pdb=" CD1 LEU B 158 " model vdw 2.146 3.460 nonbonded pdb=" O LEU C 158 " pdb=" CD1 LEU C 158 " model vdw 2.147 3.460 nonbonded pdb=" O LEU D 158 " pdb=" CD1 LEU D 158 " model vdw 2.147 3.460 nonbonded pdb=" O LEU A 158 " pdb=" CD1 LEU A 158 " model vdw 2.148 3.460 nonbonded pdb=" O GLY C 293 " pdb=" NZ LYS C 298 " model vdw 2.202 2.520 ... (remaining 94276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 group one per residue 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 3.330 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 34.790 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4769 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 : 0.005 0.109 12568 Z= 0.335 Angle : 1.119 10.082 17140 Z= 0.582 Chirality : 0.057 0.295 2052 Planarity : 0.007 0.049 2100 Dihedral : 14.475 143.388 4640 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.06 (0.20), residues: 1512 helix: -1.65 (0.15), residues: 908 sheet: -0.84 (0.58), residues: 88 loop : -2.70 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 264 HIS 0.024 0.003 HIS B 232 PHE 0.016 0.002 PHE C 309 TYR 0.023 0.002 TYR A 404 ARG 0.010 0.001 ARG D 391 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8709 (mt) cc_final: 0.7996 (mt) REVERT: A 104 LEU cc_start: 0.7719 (pp) cc_final: 0.6954 (mm) REVERT: A 224 LYS cc_start: 0.1293 (tmtt) cc_final: 0.0869 (ttmt) REVERT: A 235 ARG cc_start: 0.6404 (mtp180) cc_final: 0.5637 (mmt180) REVERT: A 261 ASP cc_start: 0.7496 (m-30) cc_final: 0.7021 (m-30) REVERT: A 353 GLU cc_start: 0.8267 (tp30) cc_final: 0.8042 (tm-30) REVERT: A 390 TYR cc_start: 0.6292 (m-80) cc_final: 0.5535 (m-80) REVERT: B 40 PHE cc_start: 0.7031 (t80) cc_final: 0.6792 (t80) REVERT: B 100 LEU cc_start: 0.8651 (mt) cc_final: 0.8304 (mt) REVERT: B 312 ASP cc_start: 0.6036 (m-30) cc_final: 0.5721 (p0) REVERT: B 313 ILE cc_start: 0.6768 (pt) cc_final: 0.6559 (pt) REVERT: B 329 ILE cc_start: 0.5495 (pt) cc_final: 0.5118 (pt) REVERT: B 339 TYR cc_start: 0.4402 (m-10) cc_final: 0.3798 (m-80) REVERT: B 414 LEU cc_start: 0.6641 (tt) cc_final: 0.6232 (mm) REVERT: C 29 ARG cc_start: 0.6152 (tmt170) cc_final: 0.4951 (mpt180) REVERT: C 39 LEU cc_start: 0.7503 (mm) cc_final: 0.7277 (mp) REVERT: C 81 ARG cc_start: 0.0610 (ptt180) cc_final: 0.0184 (ptt180) REVERT: C 261 ASP cc_start: 0.7545 (m-30) cc_final: 0.6868 (m-30) REVERT: C 390 TYR cc_start: 0.5832 (m-80) cc_final: 0.5351 (m-80) REVERT: D 29 ARG cc_start: 0.6304 (tmt170) cc_final: 0.5128 (mpt180) REVERT: D 40 PHE cc_start: 0.7359 (t80) cc_final: 0.7134 (t80) REVERT: D 81 ARG cc_start: 0.0895 (ptt180) cc_final: 0.0589 (ptt180) REVERT: D 100 LEU cc_start: 0.8646 (mt) cc_final: 0.8257 (mt) REVERT: D 104 LEU cc_start: 0.7700 (pp) cc_final: 0.7010 (mm) REVERT: D 235 ARG cc_start: 0.6488 (mtp180) cc_final: 0.5768 (mmt180) REVERT: D 261 ASP cc_start: 0.7688 (m-30) cc_final: 0.7018 (m-30) REVERT: D 390 TYR cc_start: 0.6500 (m-80) cc_final: 0.5929 (m-80) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.2738 time to fit residues: 140.4891 Evaluate side-chains 211 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 0.0570 chunk 72 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN C 217 ASN C 410 GLN D 217 ASN D 410 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4931 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12568 Z= 0.220 Angle : 0.789 10.357 17140 Z= 0.380 Chirality : 0.044 0.136 2052 Planarity : 0.006 0.052 2100 Dihedral : 11.871 175.830 1752 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.08 % Allowed : 7.16 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.22 (0.21), residues: 1512 helix: -0.94 (0.16), residues: 908 sheet: -0.85 (0.56), residues: 88 loop : -2.36 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 264 HIS 0.014 0.002 HIS D 232 PHE 0.019 0.001 PHE C 242 TYR 0.024 0.002 TYR D 357 ARG 0.009 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8453 (mt) cc_final: 0.7895 (mt) REVERT: A 104 LEU cc_start: 0.7938 (pp) cc_final: 0.6994 (mm) REVERT: A 255 ARG cc_start: 0.6915 (mtt180) cc_final: 0.6714 (mtm-85) REVERT: A 261 ASP cc_start: 0.7559 (m-30) cc_final: 0.7241 (m-30) REVERT: A 353 GLU cc_start: 0.8230 (tp30) cc_final: 0.8008 (tm-30) REVERT: A 368 GLU cc_start: 0.6180 (pm20) cc_final: 0.5762 (mp0) REVERT: A 390 TYR cc_start: 0.6531 (m-80) cc_final: 0.5927 (m-80) REVERT: B 100 LEU cc_start: 0.8643 (mt) cc_final: 0.8249 (mt) REVERT: B 104 LEU cc_start: 0.8001 (pp) cc_final: 0.7274 (mm) REVERT: B 270 TYR cc_start: 0.4886 (t80) cc_final: 0.4453 (t80) REVERT: B 329 ILE cc_start: 0.5665 (pt) cc_final: 0.5349 (pt) REVERT: B 339 TYR cc_start: 0.4439 (m-10) cc_final: 0.3924 (m-80) REVERT: C 29 ARG cc_start: 0.6177 (tmt170) cc_final: 0.4900 (mpt180) REVERT: C 48 ILE cc_start: 0.8542 (tt) cc_final: 0.8340 (pt) REVERT: C 235 ARG cc_start: 0.6110 (mtp180) cc_final: 0.5665 (mpt180) REVERT: C 261 ASP cc_start: 0.7425 (m-30) cc_final: 0.7155 (m-30) REVERT: C 357 TYR cc_start: 0.5680 (m-80) cc_final: 0.5372 (m-10) REVERT: C 390 TYR cc_start: 0.5987 (m-80) cc_final: 0.5380 (m-80) REVERT: D 100 LEU cc_start: 0.8647 (mt) cc_final: 0.8292 (mt) REVERT: D 104 LEU cc_start: 0.7929 (pp) cc_final: 0.7203 (mm) REVERT: D 235 ARG cc_start: 0.5739 (mtp180) cc_final: 0.5417 (mmt180) REVERT: D 261 ASP cc_start: 0.7403 (m-30) cc_final: 0.7119 (m-30) REVERT: D 357 TYR cc_start: 0.5936 (m-80) cc_final: 0.5585 (m-80) REVERT: D 390 TYR cc_start: 0.6644 (m-80) cc_final: 0.6144 (m-80) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.2286 time to fit residues: 79.8860 Evaluate side-chains 202 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 137 optimal weight: 0.0010 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 217 ASN B 217 ASN C 217 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5052 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12568 Z= 0.308 Angle : 0.851 9.982 17140 Z= 0.409 Chirality : 0.047 0.157 2052 Planarity : 0.006 0.079 2100 Dihedral : 11.706 177.926 1752 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.15 % Allowed : 6.63 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.04 (0.21), residues: 1512 helix: -0.75 (0.17), residues: 868 sheet: -0.23 (0.57), residues: 88 loop : -2.42 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 264 HIS 0.006 0.002 HIS D 232 PHE 0.018 0.002 PHE C 242 TYR 0.017 0.002 TYR A 404 ARG 0.012 0.001 ARG D 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8492 (mt) cc_final: 0.7956 (mt) REVERT: A 104 LEU cc_start: 0.8105 (pp) cc_final: 0.7201 (mm) REVERT: A 261 ASP cc_start: 0.7467 (m-30) cc_final: 0.7185 (m-30) REVERT: A 357 TYR cc_start: 0.6685 (m-80) cc_final: 0.6244 (m-80) REVERT: A 390 TYR cc_start: 0.6477 (m-80) cc_final: 0.5781 (m-80) REVERT: B 40 PHE cc_start: 0.7343 (t80) cc_final: 0.7040 (t80) REVERT: B 261 ASP cc_start: 0.7401 (m-30) cc_final: 0.7031 (m-30) REVERT: B 270 TYR cc_start: 0.5000 (t80) cc_final: 0.4452 (t80) REVERT: B 329 ILE cc_start: 0.5614 (pt) cc_final: 0.5256 (pt) REVERT: B 339 TYR cc_start: 0.4475 (m-10) cc_final: 0.3853 (m-80) REVERT: B 357 TYR cc_start: 0.5873 (m-80) cc_final: 0.5531 (m-80) REVERT: C 235 ARG cc_start: 0.5559 (mtp180) cc_final: 0.5239 (mpt180) REVERT: C 261 ASP cc_start: 0.7218 (m-30) cc_final: 0.6998 (m-30) REVERT: C 270 TYR cc_start: 0.4983 (t80) cc_final: 0.4516 (t80) REVERT: C 366 PHE cc_start: 0.7086 (p90) cc_final: 0.6826 (p90) REVERT: C 377 ARG cc_start: 0.7737 (tpm170) cc_final: 0.7501 (tpm170) REVERT: C 384 ARG cc_start: 0.7339 (mmm-85) cc_final: 0.6605 (mmm160) REVERT: C 390 TYR cc_start: 0.6277 (m-80) cc_final: 0.5655 (m-80) REVERT: D 100 LEU cc_start: 0.8587 (mt) cc_final: 0.8138 (mt) REVERT: D 104 LEU cc_start: 0.7977 (pp) cc_final: 0.7174 (mm) REVERT: D 235 ARG cc_start: 0.5495 (mtp180) cc_final: 0.5218 (mmt180) REVERT: D 261 ASP cc_start: 0.7328 (m-30) cc_final: 0.7028 (m-30) REVERT: D 339 TYR cc_start: 0.3912 (m-10) cc_final: 0.3238 (m-80) REVERT: D 369 MET cc_start: 0.7199 (mmt) cc_final: 0.6980 (mmm) REVERT: D 390 TYR cc_start: 0.6546 (m-80) cc_final: 0.5964 (m-80) REVERT: D 391 ARG cc_start: 0.6102 (tpt-90) cc_final: 0.5580 (tpp80) outliers start: 2 outliers final: 2 residues processed: 226 average time/residue: 0.2113 time to fit residues: 71.4401 Evaluate side-chains 190 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 15 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5027 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12568 Z= 0.222 Angle : 0.760 8.963 17140 Z= 0.360 Chirality : 0.043 0.150 2052 Planarity : 0.005 0.063 2100 Dihedral : 11.175 172.981 1752 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.69 (0.22), residues: 1512 helix: -0.38 (0.18), residues: 848 sheet: -0.01 (0.57), residues: 88 loop : -2.39 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 176 HIS 0.012 0.001 HIS C 232 PHE 0.015 0.001 PHE D 242 TYR 0.019 0.001 TYR B 26 ARG 0.003 0.000 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8521 (mt) cc_final: 0.7977 (mt) REVERT: A 104 LEU cc_start: 0.8093 (pp) cc_final: 0.7265 (mp) REVERT: A 261 ASP cc_start: 0.7493 (m-30) cc_final: 0.7214 (m-30) REVERT: A 357 TYR cc_start: 0.6445 (m-80) cc_final: 0.5966 (m-80) REVERT: A 390 TYR cc_start: 0.6414 (m-80) cc_final: 0.5737 (m-80) REVERT: B 190 THR cc_start: 0.8039 (m) cc_final: 0.7608 (p) REVERT: B 261 ASP cc_start: 0.7336 (m-30) cc_final: 0.7012 (m-30) REVERT: B 270 TYR cc_start: 0.4910 (t80) cc_final: 0.4458 (t80) REVERT: B 329 ILE cc_start: 0.5611 (pt) cc_final: 0.5272 (pt) REVERT: B 339 TYR cc_start: 0.4455 (m-10) cc_final: 0.4245 (m-80) REVERT: B 357 TYR cc_start: 0.5904 (m-80) cc_final: 0.5489 (m-80) REVERT: B 372 ILE cc_start: 0.7479 (tp) cc_final: 0.7272 (tp) REVERT: C 261 ASP cc_start: 0.7198 (m-30) cc_final: 0.6971 (m-30) REVERT: C 340 PHE cc_start: 0.7601 (m-10) cc_final: 0.7321 (m-10) REVERT: C 366 PHE cc_start: 0.7104 (p90) cc_final: 0.6813 (p90) REVERT: C 390 TYR cc_start: 0.6230 (m-80) cc_final: 0.5556 (m-80) REVERT: D 100 LEU cc_start: 0.8626 (mt) cc_final: 0.8421 (mt) REVERT: D 235 ARG cc_start: 0.5589 (mtp180) cc_final: 0.5288 (mmt180) REVERT: D 261 ASP cc_start: 0.7213 (m-30) cc_final: 0.6930 (m-30) REVERT: D 340 PHE cc_start: 0.7840 (m-10) cc_final: 0.7453 (m-10) REVERT: D 357 TYR cc_start: 0.6153 (m-80) cc_final: 0.5946 (m-80) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1868 time to fit residues: 61.2720 Evaluate side-chains 187 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 0.0980 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN D 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5091 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12568 Z= 0.275 Angle : 0.816 9.910 17140 Z= 0.385 Chirality : 0.046 0.168 2052 Planarity : 0.006 0.061 2100 Dihedral : 10.535 167.695 1752 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.15 % Allowed : 4.65 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.72 (0.21), residues: 1512 helix: -0.47 (0.18), residues: 868 sheet: 0.13 (0.56), residues: 88 loop : -2.37 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 264 HIS 0.007 0.002 HIS C 232 PHE 0.016 0.002 PHE B 302 TYR 0.023 0.002 TYR C 270 ARG 0.003 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8455 (mt) cc_final: 0.7850 (mt) REVERT: A 104 LEU cc_start: 0.8305 (pp) cc_final: 0.7329 (mm) REVERT: A 261 ASP cc_start: 0.7474 (m-30) cc_final: 0.7206 (m-30) REVERT: A 340 PHE cc_start: 0.7719 (m-10) cc_final: 0.7392 (m-10) REVERT: A 353 GLU cc_start: 0.8258 (tp30) cc_final: 0.7830 (tm-30) REVERT: A 357 TYR cc_start: 0.6188 (m-80) cc_final: 0.5661 (m-80) REVERT: A 369 MET cc_start: 0.6801 (mmm) cc_final: 0.6581 (mmm) REVERT: A 390 TYR cc_start: 0.6347 (m-80) cc_final: 0.5832 (m-80) REVERT: B 261 ASP cc_start: 0.7369 (m-30) cc_final: 0.7052 (m-30) REVERT: B 329 ILE cc_start: 0.5502 (pt) cc_final: 0.5184 (pt) REVERT: B 339 TYR cc_start: 0.4590 (m-10) cc_final: 0.3773 (m-80) REVERT: B 340 PHE cc_start: 0.7591 (m-80) cc_final: 0.7131 (m-80) REVERT: B 369 MET cc_start: 0.5684 (mmp) cc_final: 0.4191 (tmm) REVERT: C 261 ASP cc_start: 0.6907 (m-30) cc_final: 0.6681 (m-30) REVERT: C 366 PHE cc_start: 0.7127 (p90) cc_final: 0.6849 (p90) REVERT: C 377 ARG cc_start: 0.7777 (tpm170) cc_final: 0.7193 (tpm170) REVERT: D 100 LEU cc_start: 0.8600 (mt) cc_final: 0.8396 (mt) REVERT: D 261 ASP cc_start: 0.7228 (m-30) cc_final: 0.6932 (m-30) REVERT: D 357 TYR cc_start: 0.6147 (m-80) cc_final: 0.5825 (m-80) outliers start: 2 outliers final: 0 residues processed: 227 average time/residue: 0.1949 time to fit residues: 67.9186 Evaluate side-chains 185 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.0870 chunk 132 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.0970 chunk 36 optimal weight: 0.0470 chunk 147 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.4454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN B 364 GLN C 217 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN D 217 ASN D 232 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5048 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12568 Z= 0.186 Angle : 0.741 9.787 17140 Z= 0.345 Chirality : 0.043 0.152 2052 Planarity : 0.005 0.068 2100 Dihedral : 9.543 155.980 1752 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.62 (0.22), residues: 1512 helix: -0.31 (0.17), residues: 920 sheet: 0.26 (0.56), residues: 88 loop : -2.69 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 176 HIS 0.007 0.001 HIS C 232 PHE 0.016 0.001 PHE B 366 TYR 0.016 0.001 TYR C 270 ARG 0.005 0.000 ARG D 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8449 (mt) cc_final: 0.7856 (mt) REVERT: A 104 LEU cc_start: 0.8225 (pp) cc_final: 0.7268 (mm) REVERT: A 251 GLU cc_start: 0.6685 (tp30) cc_final: 0.6389 (tp30) REVERT: A 261 ASP cc_start: 0.7502 (m-30) cc_final: 0.7215 (m-30) REVERT: A 357 TYR cc_start: 0.6203 (m-80) cc_final: 0.5765 (m-80) REVERT: A 390 TYR cc_start: 0.6419 (m-80) cc_final: 0.5937 (m-80) REVERT: B 261 ASP cc_start: 0.7356 (m-30) cc_final: 0.7007 (m-30) REVERT: B 329 ILE cc_start: 0.5464 (pt) cc_final: 0.5163 (pt) REVERT: B 339 TYR cc_start: 0.4628 (m-10) cc_final: 0.3715 (m-80) REVERT: B 340 PHE cc_start: 0.7581 (m-80) cc_final: 0.7348 (m-80) REVERT: B 369 MET cc_start: 0.5249 (mmp) cc_final: 0.3965 (tmm) REVERT: C 91 LEU cc_start: 0.8190 (mt) cc_final: 0.7895 (mp) REVERT: C 235 ARG cc_start: 0.6341 (ttp-170) cc_final: 0.5781 (mpt180) REVERT: C 261 ASP cc_start: 0.6976 (m-30) cc_final: 0.6687 (m-30) REVERT: C 366 PHE cc_start: 0.6981 (p90) cc_final: 0.6730 (p90) REVERT: C 390 TYR cc_start: 0.6209 (m-80) cc_final: 0.5646 (m-80) REVERT: D 100 LEU cc_start: 0.8661 (mt) cc_final: 0.8460 (mt) REVERT: D 235 ARG cc_start: 0.6311 (ttp-170) cc_final: 0.5746 (mmt180) REVERT: D 261 ASP cc_start: 0.7136 (m-30) cc_final: 0.6829 (m-30) REVERT: D 357 TYR cc_start: 0.6361 (m-80) cc_final: 0.5984 (m-80) REVERT: D 389 LEU cc_start: 0.7024 (mp) cc_final: 0.6724 (tp) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1779 time to fit residues: 62.0402 Evaluate side-chains 190 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 123 optimal weight: 0.0030 chunk 82 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 67 optimal weight: 0.0170 chunk 90 optimal weight: 0.6980 overall best weight: 0.2426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 232 HIS B 217 ASN C 217 ASN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5032 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12568 Z= 0.172 Angle : 0.720 8.601 17140 Z= 0.335 Chirality : 0.043 0.150 2052 Planarity : 0.005 0.071 2100 Dihedral : 8.666 138.011 1752 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.38 (0.22), residues: 1512 helix: -0.15 (0.18), residues: 924 sheet: 0.27 (0.57), residues: 88 loop : -2.52 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.007 0.001 HIS C 232 PHE 0.012 0.001 PHE B 366 TYR 0.015 0.001 TYR D 186 ARG 0.003 0.000 ARG C 391 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8463 (mt) cc_final: 0.7897 (mt) REVERT: A 104 LEU cc_start: 0.8211 (pp) cc_final: 0.7263 (mm) REVERT: A 235 ARG cc_start: 0.6759 (ttp-170) cc_final: 0.6133 (mpt180) REVERT: A 251 GLU cc_start: 0.6999 (tp30) cc_final: 0.6644 (tp30) REVERT: A 261 ASP cc_start: 0.7404 (m-30) cc_final: 0.7101 (m-30) REVERT: A 357 TYR cc_start: 0.6258 (m-80) cc_final: 0.5676 (m-80) REVERT: A 390 TYR cc_start: 0.6390 (m-80) cc_final: 0.5881 (m-80) REVERT: B 261 ASP cc_start: 0.7137 (m-30) cc_final: 0.6795 (m-30) REVERT: B 329 ILE cc_start: 0.5509 (pt) cc_final: 0.5222 (pt) REVERT: B 339 TYR cc_start: 0.4814 (m-10) cc_final: 0.4180 (m-80) REVERT: B 340 PHE cc_start: 0.7707 (m-80) cc_final: 0.6884 (m-80) REVERT: B 357 TYR cc_start: 0.6076 (m-80) cc_final: 0.5790 (m-80) REVERT: B 369 MET cc_start: 0.4721 (mmp) cc_final: 0.3512 (tmm) REVERT: C 235 ARG cc_start: 0.6416 (ttp-170) cc_final: 0.5814 (mpt180) REVERT: C 261 ASP cc_start: 0.6965 (m-30) cc_final: 0.6673 (m-30) REVERT: C 366 PHE cc_start: 0.6977 (p90) cc_final: 0.6756 (p90) REVERT: C 377 ARG cc_start: 0.7840 (tpm170) cc_final: 0.7030 (tpm170) REVERT: C 384 ARG cc_start: 0.7527 (mmm-85) cc_final: 0.7306 (ptm160) REVERT: D 235 ARG cc_start: 0.6191 (ttp-170) cc_final: 0.5664 (mmt180) REVERT: D 261 ASP cc_start: 0.7169 (m-30) cc_final: 0.6868 (m-30) REVERT: D 357 TYR cc_start: 0.6312 (m-80) cc_final: 0.5879 (m-80) REVERT: D 366 PHE cc_start: 0.6766 (p90) cc_final: 0.6496 (p90) REVERT: D 369 MET cc_start: 0.5995 (tpt) cc_final: 0.5451 (tmm) REVERT: D 389 LEU cc_start: 0.6979 (mp) cc_final: 0.6570 (tp) REVERT: D 390 TYR cc_start: 0.6816 (m-80) cc_final: 0.6028 (m-80) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1954 time to fit residues: 64.4952 Evaluate side-chains 190 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.0000 chunk 44 optimal weight: 0.0000 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN C 410 GLN D 217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5040 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12568 Z= 0.181 Angle : 0.737 9.753 17140 Z= 0.340 Chirality : 0.043 0.148 2052 Planarity : 0.005 0.060 2100 Dihedral : 8.366 133.074 1752 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.28 (0.22), residues: 1512 helix: -0.08 (0.18), residues: 932 sheet: 0.28 (0.57), residues: 88 loop : -2.49 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.005 0.001 HIS C 232 PHE 0.013 0.001 PHE D 340 TYR 0.015 0.001 TYR C 259 ARG 0.003 0.000 ARG D 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8506 (mt) cc_final: 0.7943 (mt) REVERT: A 104 LEU cc_start: 0.8193 (pp) cc_final: 0.7203 (mm) REVERT: A 251 GLU cc_start: 0.6963 (tp30) cc_final: 0.6579 (tp30) REVERT: A 261 ASP cc_start: 0.7462 (m-30) cc_final: 0.7157 (m-30) REVERT: A 390 TYR cc_start: 0.6399 (m-80) cc_final: 0.5893 (m-80) REVERT: B 261 ASP cc_start: 0.7219 (m-30) cc_final: 0.6893 (m-30) REVERT: B 340 PHE cc_start: 0.7617 (m-80) cc_final: 0.7190 (m-80) REVERT: B 357 TYR cc_start: 0.5913 (m-80) cc_final: 0.5696 (m-80) REVERT: B 369 MET cc_start: 0.4527 (mmp) cc_final: 0.3406 (tmm) REVERT: C 235 ARG cc_start: 0.6446 (ttp-170) cc_final: 0.5808 (mpt180) REVERT: C 261 ASP cc_start: 0.7020 (m-30) cc_final: 0.6726 (m-30) REVERT: C 301 LEU cc_start: 0.7084 (tp) cc_final: 0.6750 (tp) REVERT: C 366 PHE cc_start: 0.6876 (p90) cc_final: 0.6609 (p90) REVERT: C 377 ARG cc_start: 0.7819 (tpm170) cc_final: 0.6917 (tpm170) REVERT: D 235 ARG cc_start: 0.6263 (ttp-170) cc_final: 0.5681 (mmt180) REVERT: D 261 ASP cc_start: 0.7169 (m-30) cc_final: 0.6861 (m-30) REVERT: D 357 TYR cc_start: 0.6268 (m-80) cc_final: 0.5807 (m-80) REVERT: D 369 MET cc_start: 0.6069 (tpt) cc_final: 0.5178 (tmm) REVERT: D 389 LEU cc_start: 0.6999 (mp) cc_final: 0.6544 (tp) REVERT: D 390 TYR cc_start: 0.6787 (m-80) cc_final: 0.6012 (m-80) REVERT: D 413 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8268 (mm-30) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2007 time to fit residues: 64.6983 Evaluate side-chains 189 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 82 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 0.0370 chunk 41 optimal weight: 0.0470 chunk 123 optimal weight: 5.9990 chunk 129 optimal weight: 0.0270 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5028 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12568 Z= 0.169 Angle : 0.728 10.039 17140 Z= 0.334 Chirality : 0.043 0.148 2052 Planarity : 0.005 0.061 2100 Dihedral : 8.203 130.859 1752 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.22), residues: 1512 helix: 0.06 (0.18), residues: 928 sheet: 0.15 (0.57), residues: 88 loop : -2.48 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 176 HIS 0.006 0.001 HIS C 232 PHE 0.010 0.001 PHE D 340 TYR 0.014 0.001 TYR C 259 ARG 0.003 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8533 (mt) cc_final: 0.7996 (mt) REVERT: A 104 LEU cc_start: 0.8189 (pp) cc_final: 0.7239 (mm) REVERT: A 251 GLU cc_start: 0.6953 (tp30) cc_final: 0.6562 (tp30) REVERT: A 261 ASP cc_start: 0.7447 (m-30) cc_final: 0.7149 (m-30) REVERT: A 390 TYR cc_start: 0.6381 (m-80) cc_final: 0.5870 (m-80) REVERT: B 261 ASP cc_start: 0.7125 (m-30) cc_final: 0.6783 (m-30) REVERT: B 340 PHE cc_start: 0.7429 (m-80) cc_final: 0.7091 (m-80) REVERT: B 357 TYR cc_start: 0.5756 (m-80) cc_final: 0.5437 (m-80) REVERT: B 369 MET cc_start: 0.4654 (mmp) cc_final: 0.3606 (tmm) REVERT: C 235 ARG cc_start: 0.6471 (ttp-170) cc_final: 0.5811 (mpt180) REVERT: C 261 ASP cc_start: 0.7048 (m-30) cc_final: 0.6767 (m-30) REVERT: C 301 LEU cc_start: 0.7010 (tp) cc_final: 0.6758 (tp) REVERT: C 366 PHE cc_start: 0.6787 (p90) cc_final: 0.6464 (p90) REVERT: C 377 ARG cc_start: 0.7861 (tpm170) cc_final: 0.6960 (tpm170) REVERT: D 235 ARG cc_start: 0.6361 (ttp-170) cc_final: 0.5727 (mmt180) REVERT: D 261 ASP cc_start: 0.7285 (m-30) cc_final: 0.6974 (m-30) REVERT: D 357 TYR cc_start: 0.6298 (m-80) cc_final: 0.5830 (m-80) REVERT: D 371 LEU cc_start: 0.7393 (pp) cc_final: 0.7113 (tp) REVERT: D 389 LEU cc_start: 0.6929 (mp) cc_final: 0.6445 (tp) REVERT: D 390 TYR cc_start: 0.6755 (m-80) cc_final: 0.5967 (m-80) REVERT: D 413 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8336 (mm-30) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1885 time to fit residues: 62.5674 Evaluate side-chains 184 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 151 optimal weight: 0.0270 chunk 139 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 12 optimal weight: 0.0170 chunk 93 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN D 217 ASN D 292 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5049 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 12568 Z= 0.194 Angle : 0.744 9.849 17140 Z= 0.341 Chirality : 0.043 0.167 2052 Planarity : 0.005 0.057 2100 Dihedral : 8.160 130.633 1752 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.22), residues: 1512 helix: 0.06 (0.18), residues: 932 sheet: 0.13 (0.57), residues: 88 loop : -2.36 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.005 0.001 HIS C 232 PHE 0.010 0.001 PHE D 340 TYR 0.016 0.001 TYR C 259 ARG 0.003 0.000 ARG C 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8530 (mt) cc_final: 0.7981 (mt) REVERT: A 104 LEU cc_start: 0.8196 (pp) cc_final: 0.7245 (mm) REVERT: A 235 ARG cc_start: 0.5797 (mtp180) cc_final: 0.5554 (mmt180) REVERT: A 251 GLU cc_start: 0.6960 (tp30) cc_final: 0.6575 (tp30) REVERT: A 261 ASP cc_start: 0.7443 (m-30) cc_final: 0.7145 (m-30) REVERT: A 390 TYR cc_start: 0.6321 (m-80) cc_final: 0.5854 (m-80) REVERT: B 261 ASP cc_start: 0.7030 (m-30) cc_final: 0.6705 (m-30) REVERT: B 340 PHE cc_start: 0.7466 (m-80) cc_final: 0.7132 (m-80) REVERT: B 357 TYR cc_start: 0.5752 (m-80) cc_final: 0.5474 (m-80) REVERT: B 369 MET cc_start: 0.4604 (mmp) cc_final: 0.3744 (tmm) REVERT: C 235 ARG cc_start: 0.6504 (ttp-170) cc_final: 0.5818 (mpt180) REVERT: C 261 ASP cc_start: 0.6944 (m-30) cc_final: 0.6653 (m-30) REVERT: C 366 PHE cc_start: 0.6819 (p90) cc_final: 0.6477 (p90) REVERT: C 377 ARG cc_start: 0.7869 (tpm170) cc_final: 0.6932 (tpm170) REVERT: D 235 ARG cc_start: 0.6509 (ttp-170) cc_final: 0.5840 (mmt180) REVERT: D 261 ASP cc_start: 0.7305 (m-30) cc_final: 0.6996 (m-30) REVERT: D 357 TYR cc_start: 0.6302 (m-80) cc_final: 0.5823 (m-80) REVERT: D 369 MET cc_start: 0.6135 (tpt) cc_final: 0.5572 (tmm) REVERT: D 371 LEU cc_start: 0.7442 (pp) cc_final: 0.7209 (tp) REVERT: D 389 LEU cc_start: 0.6903 (mp) cc_final: 0.6401 (tp) REVERT: D 390 TYR cc_start: 0.6741 (m-80) cc_final: 0.5961 (m-80) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2089 time to fit residues: 63.3374 Evaluate side-chains 184 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 15 optimal weight: 0.0980 chunk 22 optimal weight: 0.4980 chunk 106 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN D 217 ASN D 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.239711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.214189 restraints weight = 141815.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.219439 restraints weight = 76906.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.218434 restraints weight = 58695.662| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.7235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 12568 Z= 0.289 Angle : 0.812 10.702 17140 Z= 0.379 Chirality : 0.046 0.156 2052 Planarity : 0.006 0.049 2100 Dihedral : 8.336 131.314 1752 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.21), residues: 1512 helix: -0.06 (0.17), residues: 908 sheet: 0.15 (0.58), residues: 88 loop : -2.28 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 264 HIS 0.005 0.001 HIS A 281 PHE 0.014 0.002 PHE B 302 TYR 0.019 0.002 TYR C 259 ARG 0.005 0.001 ARG D 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2377.62 seconds wall clock time: 43 minutes 38.15 seconds (2618.15 seconds total)