Starting phenix.real_space_refine on Thu Mar 6 00:03:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otj_17181/03_2025/8otj_17181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otj_17181/03_2025/8otj_17181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8otj_17181/03_2025/8otj_17181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otj_17181/03_2025/8otj_17181.map" model { file = "/net/cci-nas-00/data/ceres_data/8otj_17181/03_2025/8otj_17181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otj_17181/03_2025/8otj_17181.cif" } resolution = 3.3 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= 0.003 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: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 2569 2.51 5 N 756 2.21 5 O 777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4109 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 2.61, per 1000 atoms: 0.64 Number of scatterers: 4109 At special positions: 0 Unit cell: (132.986, 108.206, 40.474, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 777 8.00 N 756 7.00 C 2569 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=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 468.6 milliseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 48.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.251A pdb=" N VAL A 306 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL B 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 7.043A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 324 removed outlier: 6.303A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LYS B 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N SER A 320 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY B 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N CYS A 322 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER E 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER F 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.072A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.432A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 346 removed outlier: 6.557A pdb=" N LEU A 344 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 349 through 359 removed outlier: 6.342A pdb=" N VAL A 350 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LYS B 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER A 352 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY B 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LEU B 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N SER A 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N ASN B 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N ASP A 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER E 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU A 357 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP E 358 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A 359 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER F 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU E 357 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP F 358 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN E 359 " --> pdb=" O ASP F 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.366A pdb=" N ASN A 368 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE B 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS A 370 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N THR B 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU A 372 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 378 through 379 removed outlier: 6.560A pdb=" N PHE A 378 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.251A pdb=" N VAL C 306 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL G 309 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 308 " --> pdb=" O VAL G 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 7.044A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 324 removed outlier: 6.802A pdb=" N SER D 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL C 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LYS G 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER C 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY G 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N CYS C 322 " --> pdb=" O GLY G 323 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.073A pdb=" N ILE C 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 336 through 340 removed outlier: 6.431A pdb=" N VAL C 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS G 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C 339 " --> pdb=" O LYS G 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 343 through 346 removed outlier: 6.558A pdb=" N LEU C 344 " --> pdb=" O ASP G 345 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 349 through 359 removed outlier: 6.783A pdb=" N SER D 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 357 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP D 358 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C 359 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL C 350 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LYS G 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER C 352 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLY G 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE C 354 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LEU G 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N SER C 356 " --> pdb=" O LEU G 357 " (cutoff:3.500A) removed outlier: 10.593A pdb=" N ASN G 359 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 9.431A pdb=" N ASP C 358 " --> pdb=" O ASN G 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.365A pdb=" N ASN C 368 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE G 371 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS C 370 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N THR G 373 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU C 372 " --> pdb=" O THR G 373 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 378 through 379 removed outlier: 6.560A pdb=" N PHE C 378 " --> pdb=" O ARG G 379 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 285 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: 0.90 Time building geometry restraints manager: 0.97 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: 1175 1.34 - 1.46: 973 1.46 - 1.58: 2017 1.58 - 1.70: 0 1.70 - 1.82: 7 Bond restraints: 4172 Sorted by residual: bond pdb=" C LYS D 331 " pdb=" N PRO D 332 " ideal model delta sigma weight residual 1.331 1.364 -0.032 1.28e-02 6.10e+03 6.39e+00 bond pdb=" C LYS B 331 " pdb=" N PRO B 332 " ideal model delta sigma weight residual 1.331 1.364 -0.032 1.28e-02 6.10e+03 6.32e+00 bond pdb=" C LYS E 331 " pdb=" N PRO E 332 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.28e-02 6.10e+03 6.24e+00 bond pdb=" C LYS G 331 " pdb=" N PRO G 332 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.28e-02 6.10e+03 6.23e+00 bond pdb=" C LYS A 331 " pdb=" N PRO A 332 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.28e-02 6.10e+03 6.21e+00 ... (remaining 4167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 4244 1.87 - 3.73: 1006 3.73 - 5.60: 287 5.60 - 7.47: 21 7.47 - 9.34: 21 Bond angle restraints: 5579 Sorted by residual: angle pdb=" C LYS E 321 " pdb=" CA LYS E 321 " pdb=" CB LYS E 321 " ideal model delta sigma weight residual 109.53 118.87 -9.34 1.65e+00 3.67e-01 3.20e+01 angle pdb=" C LYS B 321 " pdb=" CA LYS B 321 " pdb=" CB LYS B 321 " ideal model delta sigma weight residual 109.53 118.85 -9.32 1.65e+00 3.67e-01 3.19e+01 angle pdb=" C LYS F 321 " pdb=" CA LYS F 321 " pdb=" CB LYS F 321 " ideal model delta sigma weight residual 109.53 118.85 -9.32 1.65e+00 3.67e-01 3.19e+01 angle pdb=" C LYS D 321 " pdb=" CA LYS D 321 " pdb=" CB LYS D 321 " ideal model delta sigma weight residual 109.53 118.85 -9.32 1.65e+00 3.67e-01 3.19e+01 angle pdb=" C LYS A 321 " pdb=" CA LYS A 321 " pdb=" CB LYS A 321 " ideal model delta sigma weight residual 109.53 118.84 -9.31 1.65e+00 3.67e-01 3.19e+01 ... (remaining 5574 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 12.37: 2058 12.37 - 24.74: 301 24.74 - 37.10: 98 37.10 - 49.47: 49 49.47 - 61.84: 35 Dihedral angle restraints: 2541 sinusoidal: 1064 harmonic: 1477 Sorted by residual: dihedral pdb=" CA VAL E 318 " pdb=" C VAL E 318 " pdb=" N THR E 319 " pdb=" CA THR E 319 " ideal model delta harmonic sigma weight residual -180.00 -144.72 -35.28 0 5.00e+00 4.00e-02 4.98e+01 dihedral pdb=" CA VAL G 318 " pdb=" C VAL G 318 " pdb=" N THR G 319 " pdb=" CA THR G 319 " ideal model delta harmonic sigma weight residual -180.00 -144.73 -35.27 0 5.00e+00 4.00e-02 4.98e+01 dihedral pdb=" CA VAL A 318 " pdb=" C VAL A 318 " pdb=" N THR A 319 " pdb=" CA THR A 319 " ideal model delta harmonic sigma weight residual -180.00 -144.76 -35.24 0 5.00e+00 4.00e-02 4.97e+01 ... (remaining 2538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 282 0.066 - 0.133: 229 0.133 - 0.199: 63 0.199 - 0.265: 35 0.265 - 0.331: 14 Chirality restraints: 623 Sorted by residual: chirality pdb=" CA ASP F 348 " pdb=" N ASP F 348 " pdb=" C ASP F 348 " pdb=" CB ASP F 348 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA ASP E 348 " pdb=" N ASP E 348 " pdb=" C ASP E 348 " pdb=" CB ASP E 348 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA ASP G 348 " pdb=" N ASP G 348 " pdb=" C ASP G 348 " pdb=" CB ASP G 348 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 620 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 331 " -0.016 2.00e-02 2.50e+03 3.07e-02 9.40e+00 pdb=" C LYS E 331 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS E 331 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO E 332 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 331 " 0.016 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C LYS G 331 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS G 331 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO G 332 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 331 " 0.016 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C LYS D 331 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS D 331 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO D 332 " 0.018 2.00e-02 2.50e+03 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1330 2.90 - 3.40: 3897 3.40 - 3.90: 6454 3.90 - 4.40: 6775 4.40 - 4.90: 14122 Nonbonded interactions: 32578 Sorted by model distance: nonbonded pdb=" NZ LYS B 353 " pdb=" OD2 ASP B 358 " model vdw 2.400 3.120 nonbonded pdb=" NZ LYS C 353 " pdb=" OD2 ASP C 358 " model vdw 2.401 3.120 nonbonded pdb=" NZ LYS E 353 " pdb=" OD2 ASP E 358 " model vdw 2.401 3.120 nonbonded pdb=" NZ LYS A 353 " pdb=" OD2 ASP A 358 " model vdw 2.401 3.120 nonbonded pdb=" NZ LYS G 353 " pdb=" OD2 ASP G 358 " model vdw 2.401 3.120 ... (remaining 32573 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 10.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.090 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.008 0.034 4172 Z= 0.547 Angle : 1.799 9.336 5579 Z= 1.104 Chirality : 0.107 0.331 623 Planarity : 0.012 0.081 714 Dihedral : 16.482 61.835 1603 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 4.48 % Allowed : 8.96 % Favored : 86.57 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.37 % 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: -5.06 (0.19), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.14), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 330 PHE 0.024 0.008 PHE G 346 TYR 0.014 0.006 TYR C 310 ARG 0.012 0.003 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.497 Fit side-chains REVERT: A 305 SER cc_start: 0.8851 (p) cc_final: 0.8301 (p) REVERT: A 307 GLN cc_start: 0.8799 (mt0) cc_final: 0.8352 (mp10) REVERT: A 317 LYS cc_start: 0.7707 (ptmt) cc_final: 0.7347 (ptpp) REVERT: A 321 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8077 (mttp) REVERT: A 342 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8266 (mm-30) REVERT: A 347 LYS cc_start: 0.8597 (tttt) cc_final: 0.8382 (mtpt) REVERT: B 307 GLN cc_start: 0.8680 (mt0) cc_final: 0.8462 (mp10) REVERT: B 317 LYS cc_start: 0.7882 (ptmt) cc_final: 0.7589 (ptpp) REVERT: B 321 LYS cc_start: 0.8413 (mtpt) cc_final: 0.8142 (mttm) REVERT: B 347 LYS cc_start: 0.8481 (tttt) cc_final: 0.8160 (mtpt) REVERT: B 369 LYS cc_start: 0.9030 (ptpt) cc_final: 0.8773 (ptpp) REVERT: C 305 SER cc_start: 0.8744 (p) cc_final: 0.8195 (p) REVERT: C 307 GLN cc_start: 0.8748 (mt0) cc_final: 0.8358 (mp10) REVERT: C 317 LYS cc_start: 0.7806 (ptmt) cc_final: 0.7425 (ptpp) REVERT: C 342 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8295 (mm-30) REVERT: C 347 LYS cc_start: 0.8334 (tttt) cc_final: 0.8064 (mtpt) REVERT: D 307 GLN cc_start: 0.9169 (mt0) cc_final: 0.8857 (tm-30) REVERT: D 317 LYS cc_start: 0.8231 (ptmt) cc_final: 0.7901 (ptpp) REVERT: D 321 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8330 (mttp) REVERT: D 342 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7944 (pm20) REVERT: E 305 SER cc_start: 0.8822 (p) cc_final: 0.8476 (p) REVERT: E 307 GLN cc_start: 0.8776 (mt0) cc_final: 0.8348 (tm-30) REVERT: E 317 LYS cc_start: 0.7736 (ptmt) cc_final: 0.7481 (ptpp) REVERT: E 321 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8104 (mttp) REVERT: E 342 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8352 (mm-30) REVERT: E 347 LYS cc_start: 0.8597 (tttt) cc_final: 0.8282 (mtpt) REVERT: F 305 SER cc_start: 0.9146 (p) cc_final: 0.8702 (p) REVERT: F 307 GLN cc_start: 0.9000 (mt0) cc_final: 0.8795 (mp10) REVERT: F 317 LYS cc_start: 0.8225 (ptmt) cc_final: 0.7972 (ptpp) REVERT: F 338 GLU cc_start: 0.8259 (tt0) cc_final: 0.8020 (mt-10) REVERT: F 342 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7993 (pm20) REVERT: G 305 SER cc_start: 0.8590 (p) cc_final: 0.7920 (p) REVERT: G 307 GLN cc_start: 0.8662 (mt0) cc_final: 0.8446 (mp10) REVERT: G 317 LYS cc_start: 0.7951 (ptmt) cc_final: 0.7710 (ptpp) REVERT: G 369 LYS cc_start: 0.8969 (ptpt) cc_final: 0.8604 (ptpp) outliers start: 21 outliers final: 4 residues processed: 135 average time/residue: 0.2966 time to fit residues: 45.6349 Evaluate side-chains 68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 373 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN A 362 HIS ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN B 362 HIS ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN C 362 HIS ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN E 362 HIS ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 351 GLN G 362 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.108116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.089857 restraints weight = 6991.423| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 3.47 r_work: 0.3858 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4172 Z= 0.269 Angle : 0.699 7.937 5579 Z= 0.343 Chirality : 0.049 0.127 623 Planarity : 0.003 0.016 714 Dihedral : 5.652 16.792 557 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.43 % Allowed : 13.22 % Favored : 86.35 % 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: -4.17 (0.23), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.17), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 374 PHE 0.013 0.002 PHE E 378 TYR 0.007 0.002 TYR G 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.384 Fit side-chains REVERT: A 307 GLN cc_start: 0.7943 (mt0) cc_final: 0.7427 (tm-30) REVERT: B 307 GLN cc_start: 0.8049 (mt0) cc_final: 0.7746 (mp10) REVERT: B 342 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6755 (mm-30) REVERT: D 342 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7559 (pm20) REVERT: E 305 SER cc_start: 0.8847 (p) cc_final: 0.8558 (p) REVERT: E 307 GLN cc_start: 0.8067 (mt0) cc_final: 0.7758 (tm-30) REVERT: F 305 SER cc_start: 0.8890 (p) cc_final: 0.8192 (p) REVERT: F 307 GLN cc_start: 0.8590 (mt0) cc_final: 0.8261 (mp10) REVERT: F 338 GLU cc_start: 0.7896 (tt0) cc_final: 0.7598 (mt-10) REVERT: F 342 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7791 (pm20) outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.1835 time to fit residues: 16.1097 Evaluate side-chains 55 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain D residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.116474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.097568 restraints weight = 7080.695| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.54 r_work: 0.3903 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4172 Z= 0.194 Angle : 0.604 8.012 5579 Z= 0.293 Chirality : 0.047 0.121 623 Planarity : 0.002 0.014 714 Dihedral : 4.725 14.660 553 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.21 % Allowed : 13.86 % Favored : 85.93 % 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: -3.52 (0.26), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.20), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 374 PHE 0.009 0.002 PHE E 378 TYR 0.005 0.002 TYR D 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.547 Fit side-chains REVERT: C 311 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8496 (mtpt) REVERT: C 342 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7230 (mm-30) REVERT: D 342 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7469 (pm20) REVERT: E 307 GLN cc_start: 0.7968 (mt0) cc_final: 0.7653 (tm-30) REVERT: F 342 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7630 (pm20) REVERT: G 344 LEU cc_start: 0.9029 (mp) cc_final: 0.8801 (mp) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.2071 time to fit residues: 15.3110 Evaluate side-chains 52 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.102896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.085095 restraints weight = 7498.149| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 3.50 r_work: 0.3777 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4172 Z= 0.360 Angle : 0.674 6.590 5579 Z= 0.338 Chirality : 0.049 0.121 623 Planarity : 0.003 0.019 714 Dihedral : 5.099 18.325 553 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.20 % Allowed : 11.73 % Favored : 85.07 % 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: -3.41 (0.27), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 374 PHE 0.008 0.002 PHE E 378 TYR 0.006 0.002 TYR F 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8684 (tt0) cc_final: 0.8467 (tt0) REVERT: B 305 SER cc_start: 0.8803 (p) cc_final: 0.8544 (p) REVERT: C 342 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7249 (mm-30) REVERT: D 342 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7490 (pm20) REVERT: E 307 GLN cc_start: 0.7899 (mt0) cc_final: 0.7684 (tm-30) REVERT: E 347 LYS cc_start: 0.8071 (tttt) cc_final: 0.7611 (mttt) REVERT: F 342 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7657 (pm20) outliers start: 15 outliers final: 8 residues processed: 62 average time/residue: 0.2657 time to fit residues: 20.6753 Evaluate side-chains 64 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain G residue 305 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 16 optimal weight: 0.0060 chunk 14 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 overall best weight: 3.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.102716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.084850 restraints weight = 7686.090| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.54 r_work: 0.3769 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4172 Z= 0.353 Angle : 0.655 7.468 5579 Z= 0.329 Chirality : 0.049 0.133 623 Planarity : 0.002 0.016 714 Dihedral : 5.127 18.417 553 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.77 % Allowed : 13.65 % Favored : 83.58 % 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: -3.33 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 374 PHE 0.007 0.002 PHE E 378 TYR 0.003 0.001 TYR D 310 ARG 0.000 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.510 Fit side-chains REVERT: B 307 GLN cc_start: 0.7547 (mp10) cc_final: 0.7155 (mp10) REVERT: C 342 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7224 (mm-30) REVERT: D 342 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7570 (pm20) REVERT: E 307 GLN cc_start: 0.7942 (mt0) cc_final: 0.7560 (mp10) REVERT: E 347 LYS cc_start: 0.8135 (tttt) cc_final: 0.7666 (mttt) REVERT: F 342 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7606 (pm20) REVERT: G 307 GLN cc_start: 0.8268 (mt0) cc_final: 0.7835 (mp10) outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.1640 time to fit residues: 13.1769 Evaluate side-chains 64 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain G residue 305 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 12 optimal weight: 0.0870 chunk 1 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** 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 = 0.4236 r_free = 0.4236 target = 0.106184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.088058 restraints weight = 7242.563| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 3.53 r_work: 0.3828 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4172 Z= 0.207 Angle : 0.588 8.498 5579 Z= 0.282 Chirality : 0.047 0.118 623 Planarity : 0.002 0.012 714 Dihedral : 4.637 16.145 553 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.13 % Allowed : 15.14 % Favored : 82.73 % 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: -3.09 (0.29), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 374 PHE 0.006 0.001 PHE E 378 TYR 0.003 0.001 TYR D 310 ARG 0.000 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.555 Fit side-chains REVERT: A 342 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7376 (mm-30) REVERT: B 307 GLN cc_start: 0.7557 (mp10) cc_final: 0.7153 (mp10) REVERT: D 342 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7568 (pm20) REVERT: E 307 GLN cc_start: 0.7947 (mt0) cc_final: 0.7567 (mp10) REVERT: E 347 LYS cc_start: 0.8103 (tttt) cc_final: 0.7660 (mttt) REVERT: F 342 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7644 (pm20) REVERT: G 307 GLN cc_start: 0.8224 (mt0) cc_final: 0.7967 (mp10) outliers start: 10 outliers final: 8 residues processed: 63 average time/residue: 0.2253 time to fit residues: 18.1762 Evaluate side-chains 65 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 373 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** 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 = 0.4235 r_free = 0.4235 target = 0.106137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.087963 restraints weight = 7348.518| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.56 r_work: 0.3821 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4172 Z= 0.228 Angle : 0.581 9.049 5579 Z= 0.282 Chirality : 0.047 0.118 623 Planarity : 0.002 0.013 714 Dihedral : 4.532 15.605 553 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.35 % Allowed : 15.78 % Favored : 81.88 % 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: -3.02 (0.30), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 374 PHE 0.005 0.002 PHE E 378 TYR 0.003 0.001 TYR C 310 ARG 0.000 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.455 Fit side-chains REVERT: A 342 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7388 (mm-30) REVERT: B 307 GLN cc_start: 0.7567 (mp10) cc_final: 0.7144 (mp10) REVERT: B 342 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6766 (mp0) REVERT: D 342 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7602 (pm20) REVERT: E 307 GLN cc_start: 0.7919 (mt0) cc_final: 0.7654 (mp10) REVERT: E 347 LYS cc_start: 0.8200 (tttt) cc_final: 0.7764 (mttt) REVERT: F 342 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7664 (pm20) REVERT: G 307 GLN cc_start: 0.8239 (mt0) cc_final: 0.7976 (mp10) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.1563 time to fit residues: 12.5491 Evaluate side-chains 69 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 373 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 43 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 39 optimal weight: 0.0970 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** 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 = 0.4194 r_free = 0.4194 target = 0.103598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.085720 restraints weight = 7365.500| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.51 r_work: 0.3787 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4172 Z= 0.304 Angle : 0.627 9.054 5579 Z= 0.306 Chirality : 0.048 0.118 623 Planarity : 0.002 0.016 714 Dihedral : 4.767 16.617 553 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.77 % Allowed : 16.20 % Favored : 81.02 % 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 (0.30), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 374 PHE 0.006 0.002 PHE E 378 TYR 0.004 0.001 TYR C 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.523 Fit side-chains REVERT: A 342 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7467 (mm-30) REVERT: B 307 GLN cc_start: 0.7547 (mp10) cc_final: 0.7123 (mp10) REVERT: B 342 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6811 (mm-30) REVERT: D 342 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7608 (pm20) REVERT: D 380 GLU cc_start: 0.6382 (tm-30) cc_final: 0.6029 (tp30) REVERT: E 307 GLN cc_start: 0.7954 (mt0) cc_final: 0.7651 (mp10) REVERT: E 347 LYS cc_start: 0.8158 (tttt) cc_final: 0.7681 (mttm) REVERT: F 342 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7899 (pm20) REVERT: G 307 GLN cc_start: 0.8244 (mt0) cc_final: 0.7982 (mp10) outliers start: 13 outliers final: 11 residues processed: 67 average time/residue: 0.1627 time to fit residues: 13.9877 Evaluate side-chains 73 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 25 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 0.0040 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** 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 = 0.4198 r_free = 0.4198 target = 0.103808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.085735 restraints weight = 7367.073| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.53 r_work: 0.3789 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4172 Z= 0.285 Angle : 0.622 9.213 5579 Z= 0.304 Chirality : 0.048 0.118 623 Planarity : 0.002 0.014 714 Dihedral : 4.755 16.425 553 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.77 % Allowed : 15.99 % Favored : 81.24 % 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: -3.01 (0.30), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 374 PHE 0.006 0.002 PHE E 378 TYR 0.003 0.001 TYR C 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.463 Fit side-chains REVERT: A 342 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7451 (mm-30) REVERT: B 342 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6795 (mm-30) REVERT: D 342 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7623 (pm20) REVERT: E 307 GLN cc_start: 0.7950 (mt0) cc_final: 0.7659 (mp10) REVERT: E 347 LYS cc_start: 0.8179 (tttt) cc_final: 0.7705 (mttm) REVERT: F 342 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7661 (pm20) REVERT: G 307 GLN cc_start: 0.8231 (mt0) cc_final: 0.7895 (mp10) outliers start: 13 outliers final: 11 residues processed: 72 average time/residue: 0.1622 time to fit residues: 14.7095 Evaluate side-chains 77 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 9.9990 chunk 45 optimal weight: 0.0270 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** 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 = 0.4236 r_free = 0.4236 target = 0.106121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.087510 restraints weight = 7177.681| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 3.55 r_work: 0.3819 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4172 Z= 0.227 Angle : 0.633 9.442 5579 Z= 0.305 Chirality : 0.047 0.119 623 Planarity : 0.002 0.017 714 Dihedral : 4.515 15.335 553 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.56 % Allowed : 16.20 % Favored : 81.24 % 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: -2.92 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 374 PHE 0.006 0.001 PHE F 378 TYR 0.002 0.001 TYR C 310 ARG 0.001 0.000 ARG D 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.490 Fit side-chains REVERT: A 342 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7452 (mm-30) REVERT: A 380 GLU cc_start: 0.6768 (tm-30) cc_final: 0.5832 (tp30) REVERT: B 307 GLN cc_start: 0.7555 (mp10) cc_final: 0.7288 (mp10) REVERT: B 342 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6792 (mm-30) REVERT: B 380 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6586 (tp30) REVERT: D 342 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7589 (pm20) REVERT: D 380 GLU cc_start: 0.6914 (tm-30) cc_final: 0.5864 (tp30) REVERT: E 307 GLN cc_start: 0.7926 (mt0) cc_final: 0.7644 (mp10) REVERT: E 347 LYS cc_start: 0.8174 (tttt) cc_final: 0.7709 (mttm) REVERT: F 342 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7630 (pm20) REVERT: G 307 GLN cc_start: 0.8216 (mt0) cc_final: 0.7944 (mp10) outliers start: 12 outliers final: 11 residues processed: 74 average time/residue: 0.1471 time to fit residues: 14.0015 Evaluate side-chains 79 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.0170 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** 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 = 0.4247 r_free = 0.4247 target = 0.106803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.088234 restraints weight = 7131.883| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.54 r_work: 0.3835 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4172 Z= 0.231 Angle : 0.646 9.480 5579 Z= 0.307 Chirality : 0.047 0.118 623 Planarity : 0.002 0.020 714 Dihedral : 4.428 14.972 553 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.13 % Allowed : 17.06 % Favored : 80.81 % 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: -2.87 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 374 PHE 0.005 0.001 PHE E 378 TYR 0.002 0.001 TYR C 310 ARG 0.001 0.000 ARG E 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2632.96 seconds wall clock time: 48 minutes 57.86 seconds (2937.86 seconds total)