Starting phenix.real_space_refine on Thu Nov 14 05:18:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otj_17181/11_2024/8otj_17181.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otj_17181/11_2024/8otj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otj_17181/11_2024/8otj_17181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otj_17181/11_2024/8otj_17181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otj_17181/11_2024/8otj_17181.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otj_17181/11_2024/8otj_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 3.09, per 1000 atoms: 0.75 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: 0.97 Conformation dependent library (CDL) restraints added in 508.4 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: 0.60 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: 0.78 Time building geometry restraints manager: 1.13 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.880 Find NCS groups from input model: 0.110 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- 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 : 0.564 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: 0.2877 time to fit residues: 44.0523 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 : 0.538 ------------------------------------------------------------------------------- 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: 7.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.502 Fit side-chains REVERT: A 307 GLN cc_start: 0.8536 (mt0) cc_final: 0.7890 (tm-30) REVERT: A 342 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8333 (mm-30) REVERT: B 307 GLN cc_start: 0.8684 (mt0) cc_final: 0.8424 (mp10) REVERT: B 342 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7317 (mm-30) REVERT: C 342 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8384 (mm-30) REVERT: D 307 GLN cc_start: 0.9173 (mt0) cc_final: 0.8789 (tm-30) REVERT: D 342 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8030 (pm20) REVERT: E 305 SER cc_start: 0.8875 (p) cc_final: 0.8551 (p) REVERT: E 307 GLN cc_start: 0.8666 (mt0) cc_final: 0.8212 (tm-30) REVERT: F 305 SER cc_start: 0.9081 (p) cc_final: 0.8704 (p) REVERT: F 307 GLN cc_start: 0.9118 (mt0) cc_final: 0.8875 (mp10) REVERT: F 338 GLU cc_start: 0.8214 (tt0) cc_final: 0.7909 (mt-10) REVERT: F 342 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8130 (pm20) outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.1587 time to fit residues: 13.6935 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 : 0.527 ------------------------------------------------------------------------------- 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 24 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 35 optimal weight: 0.0270 chunk 33 optimal weight: 7.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- 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 ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4172 Z= 0.313 Angle : 0.662 8.306 5579 Z= 0.328 Chirality : 0.049 0.120 623 Planarity : 0.003 0.017 714 Dihedral : 5.143 15.975 553 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.35 % Allowed : 11.73 % 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: -3.68 (0.26), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.20), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.009 0.002 PHE E 378 TYR 0.006 0.002 TYR G 310 ARG 0.001 0.000 ARG B 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 66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.434 Fit side-chains REVERT: A 342 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8282 (mm-30) REVERT: A 371 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8493 (mm) REVERT: B 342 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7387 (mm-30) REVERT: C 342 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8322 (mm-30) REVERT: D 307 GLN cc_start: 0.9153 (mt0) cc_final: 0.8861 (tm-30) REVERT: D 342 GLU cc_start: 0.8687 (mt-10) cc_final: 0.7937 (pm20) REVERT: E 305 SER cc_start: 0.8942 (p) cc_final: 0.8627 (p) REVERT: E 307 GLN cc_start: 0.8583 (mt0) cc_final: 0.8178 (tm-30) REVERT: E 347 LYS cc_start: 0.8428 (tttt) cc_final: 0.8001 (mttt) REVERT: E 371 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8578 (mm) REVERT: F 305 SER cc_start: 0.9069 (p) cc_final: 0.8713 (p) REVERT: F 307 GLN cc_start: 0.9105 (mt0) cc_final: 0.8871 (mp10) REVERT: F 342 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8024 (pm20) REVERT: G 307 GLN cc_start: 0.8771 (mt0) cc_final: 0.8322 (tm-30) REVERT: G 342 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7111 (mp0) outliers start: 11 outliers final: 6 residues processed: 60 average time/residue: 0.1682 time to fit residues: 12.9253 Evaluate side-chains 62 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 371 ILE 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 371 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 0.0670 chunk 29 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.6126 ------------------------------------------------------------------------------- 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** ** F 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4172 Z= 0.339 Angle : 0.668 9.190 5579 Z= 0.329 Chirality : 0.049 0.134 623 Planarity : 0.003 0.017 714 Dihedral : 5.120 16.121 553 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.92 % Allowed : 13.22 % Favored : 84.86 % 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: -3.47 (0.27), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 374 PHE 0.008 0.002 PHE E 378 TYR 0.004 0.001 TYR F 310 ARG 0.001 0.000 ARG G 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 62 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8296 (mm-30) REVERT: A 371 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8530 (mm) REVERT: B 307 GLN cc_start: 0.8474 (mp10) cc_final: 0.8230 (mp10) REVERT: B 342 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7415 (mm-30) REVERT: C 307 GLN cc_start: 0.8563 (mt0) cc_final: 0.8303 (mp10) REVERT: C 342 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8337 (mm-30) REVERT: D 307 GLN cc_start: 0.9117 (mt0) cc_final: 0.8867 (mp10) REVERT: D 342 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8006 (pm20) REVERT: D 371 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8748 (mm) REVERT: E 347 LYS cc_start: 0.8481 (tttt) cc_final: 0.8070 (mttt) REVERT: F 307 GLN cc_start: 0.9094 (mt0) cc_final: 0.8804 (tm-30) REVERT: F 342 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8040 (pm20) outliers start: 9 outliers final: 7 residues processed: 58 average time/residue: 0.1683 time to fit residues: 12.5202 Evaluate side-chains 60 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 371 ILE 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 371 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain F residue 371 ILE 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 35 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3542 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= 0.302 Angle : 0.627 8.010 5579 Z= 0.307 Chirality : 0.048 0.126 623 Planarity : 0.002 0.014 714 Dihedral : 4.940 15.455 553 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.62 % Allowed : 14.07 % Favored : 82.30 % 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: -3.35 (0.28), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.21), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 374 PHE 0.007 0.002 PHE E 378 TYR 0.003 0.001 TYR C 310 ARG 0.001 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 73 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.510 Fit side-chains REVERT: A 342 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8328 (mm-30) REVERT: B 307 GLN cc_start: 0.8478 (mp10) cc_final: 0.8222 (mp10) REVERT: B 342 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7366 (mm-30) REVERT: C 307 GLN cc_start: 0.8562 (mt0) cc_final: 0.8301 (mp10) REVERT: C 342 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8365 (mm-30) REVERT: D 307 GLN cc_start: 0.9121 (mt0) cc_final: 0.8875 (mp10) REVERT: D 342 GLU cc_start: 0.8725 (mt-10) cc_final: 0.7994 (pm20) REVERT: D 371 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8716 (mm) REVERT: E 307 GLN cc_start: 0.8593 (mt0) cc_final: 0.8220 (mp10) REVERT: F 307 GLN cc_start: 0.9098 (mt0) cc_final: 0.8832 (tm-30) REVERT: F 342 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8039 (pm20) REVERT: G 307 GLN cc_start: 0.8776 (mt0) cc_final: 0.8535 (mp10) REVERT: G 342 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7040 (mp0) outliers start: 17 outliers final: 9 residues processed: 67 average time/residue: 0.1795 time to fit residues: 15.0466 Evaluate side-chains 66 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 371 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.4980 chunk 47 optimal weight: 0.0070 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.2800 ------------------------------------------------------------------------------- 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** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.002 0.017 4172 Z= 0.152 Angle : 0.542 7.784 5579 Z= 0.256 Chirality : 0.047 0.124 623 Planarity : 0.002 0.012 714 Dihedral : 4.312 13.564 553 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.28 % Allowed : 15.99 % 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: -3.11 (0.29), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 362 PHE 0.005 0.001 PHE E 378 TYR 0.003 0.001 TYR D 310 ARG 0.000 0.000 ARG B 349 *********************** 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 64 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: B 307 GLN cc_start: 0.8548 (mp10) cc_final: 0.8284 (mp10) REVERT: B 342 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7379 (mm-30) REVERT: C 307 GLN cc_start: 0.8576 (mt0) cc_final: 0.8339 (mp10) REVERT: C 342 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8405 (mm-30) REVERT: D 307 GLN cc_start: 0.9107 (mt0) cc_final: 0.8872 (mp10) REVERT: D 342 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8006 (pm20) REVERT: D 371 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8639 (mm) REVERT: E 307 GLN cc_start: 0.8590 (mt0) cc_final: 0.8334 (mp10) REVERT: F 342 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7994 (pm20) REVERT: G 307 GLN cc_start: 0.8790 (mt0) cc_final: 0.8527 (mp10) REVERT: G 342 GLU cc_start: 0.7458 (mp0) cc_final: 0.7027 (mp0) outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.1654 time to fit residues: 12.7685 Evaluate side-chains 56 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 0.0970 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.9384 ------------------------------------------------------------------------------- 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** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS D 330 HIS ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 ASN G 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3825 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= 0.359 Angle : 0.649 8.745 5579 Z= 0.318 Chirality : 0.049 0.118 623 Planarity : 0.003 0.018 714 Dihedral : 4.843 17.732 553 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.77 % Allowed : 15.78 % Favored : 81.45 % 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: -3.20 (0.29), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 374 PHE 0.006 0.002 PHE E 378 TYR 0.005 0.001 TYR C 310 ARG 0.001 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: 13 poor density : 57 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: C 307 GLN cc_start: 0.8603 (mt0) cc_final: 0.8353 (mp10) REVERT: C 342 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8402 (mm-30) REVERT: D 307 GLN cc_start: 0.9106 (mt0) cc_final: 0.8883 (mp10) REVERT: D 342 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8033 (pm20) REVERT: D 371 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8679 (mm) REVERT: E 307 GLN cc_start: 0.8596 (mt0) cc_final: 0.8388 (mp10) REVERT: F 342 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8212 (pm20) REVERT: G 307 GLN cc_start: 0.8776 (mt0) cc_final: 0.8462 (mp10) outliers start: 13 outliers final: 11 residues processed: 63 average time/residue: 0.1622 time to fit residues: 13.1584 Evaluate side-chains 69 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER 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 371 ILE 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 F residue 311 LYS Chi-restraints excluded: chain F residue 375 LYS 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 23 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4172 Z= 0.230 Angle : 0.593 9.256 5579 Z= 0.284 Chirality : 0.047 0.119 623 Planarity : 0.002 0.018 714 Dihedral : 4.562 15.520 553 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.56 % Allowed : 15.99 % Favored : 81.45 % 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: -3.10 (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 0.005 0.002 PHE E 378 TYR 0.003 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 69 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 380 GLU cc_start: 0.6313 (tm-30) cc_final: 0.5790 (tp30) REVERT: C 307 GLN cc_start: 0.8589 (mt0) cc_final: 0.8343 (mp10) REVERT: C 342 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8367 (mm-30) REVERT: D 307 GLN cc_start: 0.9110 (mt0) cc_final: 0.8862 (mp10) REVERT: D 342 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8058 (pm20) REVERT: D 371 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8600 (mm) REVERT: D 380 GLU cc_start: 0.6438 (tm-30) cc_final: 0.5921 (tp30) REVERT: E 307 GLN cc_start: 0.8600 (mt0) cc_final: 0.8338 (mp10) REVERT: F 342 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8052 (pm20) REVERT: G 307 GLN cc_start: 0.8799 (mt0) cc_final: 0.8519 (mp10) outliers start: 12 outliers final: 9 residues processed: 62 average time/residue: 0.1579 time to fit residues: 12.7570 Evaluate side-chains 67 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER 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 371 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 46 optimal weight: 0.0000 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.9590 ------------------------------------------------------------------------------- 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** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4172 Z= 0.290 Angle : 0.641 9.139 5579 Z= 0.307 Chirality : 0.048 0.120 623 Planarity : 0.002 0.018 714 Dihedral : 4.658 16.067 553 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.56 % Allowed : 16.42 % 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: -3.08 (0.30), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 374 PHE 0.005 0.002 PHE E 378 TYR 0.004 0.001 TYR C 310 ARG 0.001 0.000 ARG A 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 72 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 380 GLU cc_start: 0.6322 (tm-30) cc_final: 0.5567 (tp30) REVERT: B 380 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6662 (tp30) REVERT: C 307 GLN cc_start: 0.8596 (mt0) cc_final: 0.8344 (mp10) REVERT: C 342 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8411 (mm-30) REVERT: D 307 GLN cc_start: 0.9115 (mt0) cc_final: 0.8863 (mp10) REVERT: D 342 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8058 (pm20) REVERT: D 371 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8615 (mm) REVERT: E 307 GLN cc_start: 0.8598 (mt0) cc_final: 0.8381 (mp10) REVERT: F 342 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8056 (pm20) REVERT: G 307 GLN cc_start: 0.8795 (mt0) cc_final: 0.8472 (mp10) outliers start: 12 outliers final: 11 residues processed: 65 average time/residue: 0.1717 time to fit residues: 14.4207 Evaluate side-chains 72 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER 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 371 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4172 Z= 0.182 Angle : 0.611 9.168 5579 Z= 0.288 Chirality : 0.047 0.119 623 Planarity : 0.002 0.018 714 Dihedral : 4.229 13.088 553 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.49 % Allowed : 17.48 % 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: -2.91 (0.30), 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 0.002 0.001 HIS G 374 PHE 0.004 0.001 PHE F 378 TYR 0.002 0.001 TYR F 310 ARG 0.001 0.000 ARG F 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 73 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 380 GLU cc_start: 0.6346 (tm-30) cc_final: 0.5813 (tp30) REVERT: B 380 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6734 (tp30) REVERT: C 307 GLN cc_start: 0.8579 (mt0) cc_final: 0.8336 (mp10) REVERT: C 342 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8391 (mm-30) REVERT: D 307 GLN cc_start: 0.9116 (mt0) cc_final: 0.8881 (mp10) REVERT: D 342 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8034 (pm20) REVERT: D 371 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8588 (mm) REVERT: D 380 GLU cc_start: 0.6599 (tm-30) cc_final: 0.5698 (tp30) REVERT: E 307 GLN cc_start: 0.8559 (mt0) cc_final: 0.8301 (mp10) REVERT: E 380 GLU cc_start: 0.6294 (tm-30) cc_final: 0.5728 (tp30) REVERT: F 342 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8075 (pm20) REVERT: F 380 GLU cc_start: 0.6362 (tm-30) cc_final: 0.5535 (tp30) REVERT: G 307 GLN cc_start: 0.8801 (mt0) cc_final: 0.8527 (mp10) outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 0.1451 time to fit residues: 12.6160 Evaluate side-chains 68 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER 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 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain G residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 0.0970 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- 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** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** 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 = 0.4217 r_free = 0.4217 target = 0.104751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.086449 restraints weight = 7211.318| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.59 r_work: 0.3805 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4177 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= 0.299 Angle : 0.660 9.095 5579 Z= 0.316 Chirality : 0.049 0.118 623 Planarity : 0.003 0.021 714 Dihedral : 4.551 16.580 553 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % 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: -2.93 (0.30), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 374 PHE 0.005 0.002 PHE E 346 TYR 0.004 0.001 TYR C 310 ARG 0.001 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1425.07 seconds wall clock time: 31 minutes 21.51 seconds (1881.51 seconds total)