Starting phenix.real_space_refine on Wed Mar 5 19:49:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7l_18219/03_2025/8q7l_18219.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7l_18219/03_2025/8q7l_18219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q7l_18219/03_2025/8q7l_18219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7l_18219/03_2025/8q7l_18219.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7l_18219/03_2025/8q7l_18219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7l_18219/03_2025/8q7l_18219.cif" } resolution = 2.82 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 6 5.16 5 C 2124 2.51 5 N 618 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 3375 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 3.84, per 1000 atoms: 1.14 Number of scatterers: 3375 At special positions: 0 Unit cell: (127.72, 140.08, 48.616, 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 6 16.00 O 627 8.00 N 618 7.00 C 2124 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: 0.86 Conformation dependent library (CDL) restraints added in 509.5 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 54.9% 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 307 through 310 removed outlier: 6.817A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.787A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 325 removed outlier: 6.396A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.451A 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 346 removed outlier: 6.822A pdb=" N LEU A 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP B 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE A 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU C 344 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP A 345 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE C 346 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 354 removed outlier: 6.470A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.400A pdb=" N ILE A 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 368 through 378 removed outlier: 6.381A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 378 removed outlier: 6.381A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 307 through 310 removed outlier: 6.957A pdb=" N ILE D 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.748A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 325 removed outlier: 6.582A pdb=" N VAL D 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LYS E 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER D 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLY E 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS D 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU E 325 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER D 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS D 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER F 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR D 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N CYS F 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS D 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER F 324 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLY D 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.495A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 336 through 340 removed outlier: 6.553A pdb=" N VAL D 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LYS E 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL D 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 343 through 346 removed outlier: 6.530A pdb=" N LEU D 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 351 through 354 removed outlier: 6.439A pdb=" N GLN D 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE F 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS D 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.237A pdb=" N ASP D 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N THR F 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE D 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 368 through 372 Processing sheet with id=AC1, first strand: chain 'E' and resid 376 through 377 removed outlier: 6.812A pdb=" N LEU D 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 219 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: 0.84 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 935 1.33 - 1.45: 431 1.45 - 1.57: 2057 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3429 Sorted by residual: bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.79e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.74e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.67e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.47e+00 bond pdb=" CZ ARG B 379 " pdb=" NH2 ARG B 379 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.40e+00 ... (remaining 3424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 3280 1.94 - 3.88: 1106 3.88 - 5.83: 171 5.83 - 7.77: 31 7.77 - 9.71: 2 Bond angle restraints: 4590 Sorted by residual: angle pdb=" C GLY C 334 " pdb=" N GLY C 335 " pdb=" CA GLY C 335 " ideal model delta sigma weight residual 122.83 129.61 -6.78 1.21e+00 6.83e-01 3.14e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 117.91 -5.31 1.00e+00 1.00e+00 2.82e+01 angle pdb=" CA LYS B 331 " pdb=" C LYS B 331 " pdb=" N PRO B 332 " ideal model delta sigma weight residual 118.16 121.83 -3.67 7.00e-01 2.04e+00 2.74e+01 angle pdb=" OE1 GLN C 336 " pdb=" CD GLN C 336 " pdb=" NE2 GLN C 336 " ideal model delta sigma weight residual 122.60 117.57 5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" OE1 GLN B 336 " pdb=" CD GLN B 336 " pdb=" NE2 GLN B 336 " ideal model delta sigma weight residual 122.60 117.63 4.97 1.00e+00 1.00e+00 2.47e+01 ... (remaining 4585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.30: 1855 12.30 - 24.60: 174 24.60 - 36.89: 35 36.89 - 49.19: 11 49.19 - 61.49: 13 Dihedral angle restraints: 2088 sinusoidal: 873 harmonic: 1215 Sorted by residual: dihedral pdb=" C LYS E 311 " pdb=" N LYS E 311 " pdb=" CA LYS E 311 " pdb=" CB LYS E 311 " ideal model delta harmonic sigma weight residual -122.60 -135.36 12.76 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" CA VAL E 306 " pdb=" C VAL E 306 " pdb=" N GLN E 307 " pdb=" CA GLN E 307 " ideal model delta harmonic sigma weight residual 180.00 154.52 25.48 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA VAL D 306 " pdb=" C VAL D 306 " pdb=" N GLN D 307 " pdb=" CA GLN D 307 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 2085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 362 0.099 - 0.198: 124 0.198 - 0.297: 21 0.297 - 0.395: 9 0.395 - 0.494: 3 Chirality restraints: 519 Sorted by residual: chirality pdb=" CA LYS D 347 " pdb=" N LYS D 347 " pdb=" C LYS D 347 " pdb=" CB LYS D 347 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA LYS E 311 " pdb=" N LYS E 311 " pdb=" C LYS E 311 " pdb=" CB LYS E 311 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 516 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.038 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR E 310 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 374 " 0.037 2.00e-02 2.50e+03 2.76e-02 1.14e+01 pdb=" CG HIS A 374 " -0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS A 374 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS A 374 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 374 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS A 374 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 334 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLY C 334 " -0.058 2.00e-02 2.50e+03 pdb=" O GLY C 334 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY C 335 " 0.019 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 31 2.71 - 3.26: 2815 3.26 - 3.80: 4737 3.80 - 4.35: 6362 4.35 - 4.90: 11409 Nonbonded interactions: 25354 Sorted by model distance: nonbonded pdb=" NZ LYS B 343 " pdb=" OE1 GLU F 338 " model vdw 2.159 3.120 nonbonded pdb=" NZ LYS C 347 " pdb=" O GLY E 333 " model vdw 2.250 3.120 nonbonded pdb=" O LYS B 347 " pdb=" NZ LYS F 331 " model vdw 2.276 3.120 nonbonded pdb=" O LYS A 347 " pdb=" NZ LYS D 331 " model vdw 2.328 3.120 nonbonded pdb=" NZ LYS A 343 " pdb=" OE1 GLU D 338 " model vdw 2.385 3.120 ... (remaining 25349 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 306 through 378) selection = (chain 'B' and resid 306 through 378) selection = (chain 'C' and resid 306 through 378) selection = chain 'D' selection = chain 'E' 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: 2.350 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.730 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.011 0.040 3429 Z= 0.739 Angle : 1.904 9.709 4590 Z= 1.254 Chirality : 0.110 0.494 519 Planarity : 0.009 0.046 582 Dihedral : 11.675 61.489 1314 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 1.03 % 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: -2.15 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS E 330 PHE 0.033 0.010 PHE D 346 TYR 0.056 0.012 TYR E 310 ARG 0.008 0.002 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 324 SER cc_start: 0.8807 (m) cc_final: 0.8539 (t) REVERT: A 338 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6983 (tt0) REVERT: A 340 LYS cc_start: 0.7573 (mttt) cc_final: 0.7261 (mttm) REVERT: A 369 LYS cc_start: 0.7499 (ttmt) cc_final: 0.6875 (tttp) REVERT: A 370 LYS cc_start: 0.8031 (tttt) cc_final: 0.7823 (tttt) REVERT: B 311 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8273 (pttp) REVERT: B 338 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7110 (mp0) REVERT: B 340 LYS cc_start: 0.8404 (mttt) cc_final: 0.8115 (mttm) REVERT: B 369 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7533 (tttt) REVERT: C 311 LYS cc_start: 0.8560 (ttmt) cc_final: 0.7617 (mmtm) REVERT: C 356 SER cc_start: 0.7815 (t) cc_final: 0.7497 (t) REVERT: C 369 LYS cc_start: 0.7611 (ttmt) cc_final: 0.7132 (tttt) REVERT: C 370 LYS cc_start: 0.8610 (tttt) cc_final: 0.8153 (tttm) REVERT: D 353 LYS cc_start: 0.7858 (mttt) cc_final: 0.7534 (mttt) REVERT: D 358 ASP cc_start: 0.8451 (m-30) cc_final: 0.8128 (m-30) REVERT: E 311 LYS cc_start: 0.8348 (pttt) cc_final: 0.8024 (ptmt) REVERT: E 345 ASP cc_start: 0.8077 (t0) cc_final: 0.7665 (t0) REVERT: E 375 LYS cc_start: 0.7949 (tttt) cc_final: 0.7695 (ttpp) REVERT: E 378 PHE cc_start: 0.5921 (t80) cc_final: 0.5550 (t80) REVERT: F 307 GLN cc_start: 0.8121 (pt0) cc_final: 0.7274 (pm20) REVERT: F 311 LYS cc_start: 0.8162 (pttt) cc_final: 0.7782 (ttpt) REVERT: F 342 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7614 (mp0) REVERT: F 358 ASP cc_start: 0.8646 (m-30) cc_final: 0.8217 (m-30) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 1.2988 time to fit residues: 203.3868 Evaluate side-chains 111 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 HIS C 368 ASN D 330 HIS D 359 ASN E 330 HIS E 359 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.116658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.105520 restraints weight = 4398.037| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.79 r_work: 0.3470 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3429 Z= 0.204 Angle : 0.663 5.854 4590 Z= 0.330 Chirality : 0.052 0.137 519 Planarity : 0.003 0.030 582 Dihedral : 5.697 16.016 450 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.81 % Allowed : 13.18 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.009 0.002 PHE A 346 TYR 0.025 0.003 TYR D 310 ARG 0.006 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8075 (tt0) REVERT: A 340 LYS cc_start: 0.8528 (mttt) cc_final: 0.8288 (mttm) REVERT: B 311 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8625 (pttm) REVERT: B 340 LYS cc_start: 0.8817 (mttt) cc_final: 0.8547 (mttm) REVERT: C 311 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8044 (mmtm) REVERT: C 338 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8027 (tt0) REVERT: C 369 LYS cc_start: 0.8301 (ttmt) cc_final: 0.8084 (tttt) REVERT: C 370 LYS cc_start: 0.8910 (tttt) cc_final: 0.8651 (tttm) REVERT: C 375 LYS cc_start: 0.8142 (ptmt) cc_final: 0.7615 (ptpp) REVERT: E 311 LYS cc_start: 0.8611 (pttt) cc_final: 0.8199 (ptmt) REVERT: E 345 ASP cc_start: 0.8205 (t0) cc_final: 0.7821 (t70) REVERT: F 311 LYS cc_start: 0.8431 (pttt) cc_final: 0.8140 (ptmt) REVERT: F 342 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7944 (mp0) REVERT: F 349 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.8004 (mtm180) outliers start: 7 outliers final: 2 residues processed: 123 average time/residue: 1.2053 time to fit residues: 152.1442 Evaluate side-chains 102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 0.2980 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS A 362 HIS B 362 HIS C 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.110315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.099158 restraints weight = 4902.469| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.88 r_work: 0.3403 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3429 Z= 0.315 Angle : 0.689 6.307 4590 Z= 0.340 Chirality : 0.052 0.138 519 Planarity : 0.003 0.020 582 Dihedral : 5.334 15.082 450 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.81 % Allowed : 18.09 % Favored : 80.10 % 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: -2.00 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.008 0.002 PHE A 346 TYR 0.011 0.002 TYR A 310 ARG 0.004 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7981 (tt0) REVERT: A 340 LYS cc_start: 0.8552 (mttt) cc_final: 0.8316 (mttm) REVERT: A 363 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8981 (t) REVERT: B 311 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8458 (pttm) REVERT: B 338 GLU cc_start: 0.8571 (tt0) cc_final: 0.8271 (tt0) REVERT: B 340 LYS cc_start: 0.8917 (mttt) cc_final: 0.8623 (mttm) REVERT: C 311 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8176 (mmtm) REVERT: C 342 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8407 (pt0) REVERT: C 370 LYS cc_start: 0.8922 (tttt) cc_final: 0.8589 (tttm) REVERT: C 375 LYS cc_start: 0.8241 (ptmt) cc_final: 0.7954 (ptpp) REVERT: E 311 LYS cc_start: 0.8731 (pttt) cc_final: 0.8362 (ptmt) REVERT: E 345 ASP cc_start: 0.8184 (t0) cc_final: 0.7744 (t70) REVERT: E 370 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8092 (tmtt) REVERT: F 311 LYS cc_start: 0.8563 (pttt) cc_final: 0.8187 (ptmt) REVERT: F 342 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7892 (mp0) REVERT: F 343 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7968 (tttm) REVERT: F 349 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.8101 (mtm180) outliers start: 7 outliers final: 3 residues processed: 117 average time/residue: 1.3026 time to fit residues: 156.3134 Evaluate side-chains 104 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 370 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 0.0170 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.111195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.099820 restraints weight = 4753.469| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.87 r_work: 0.3413 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3429 Z= 0.210 Angle : 0.619 7.569 4590 Z= 0.298 Chirality : 0.050 0.130 519 Planarity : 0.003 0.018 582 Dihedral : 4.910 13.107 450 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.33 % Allowed : 18.60 % Favored : 79.07 % 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: -2.10 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.006 0.001 PHE D 378 TYR 0.031 0.004 TYR D 310 ARG 0.004 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.423 Fit side-chains REVERT: A 338 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7965 (tt0) REVERT: A 340 LYS cc_start: 0.8496 (mttt) cc_final: 0.8274 (mttm) REVERT: B 311 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8478 (pttm) REVERT: B 338 GLU cc_start: 0.8556 (tt0) cc_final: 0.8207 (tt0) REVERT: B 340 LYS cc_start: 0.8913 (mttt) cc_final: 0.8601 (mttm) REVERT: C 358 ASP cc_start: 0.7622 (m-30) cc_final: 0.7383 (m-30) REVERT: E 311 LYS cc_start: 0.8605 (pttt) cc_final: 0.8239 (ptmt) REVERT: E 343 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7086 (mmtt) REVERT: E 345 ASP cc_start: 0.8127 (t0) cc_final: 0.7634 (t70) REVERT: F 311 LYS cc_start: 0.8595 (pttt) cc_final: 0.8199 (ptmt) REVERT: F 342 GLU cc_start: 0.8566 (mt-10) cc_final: 0.7876 (mp0) REVERT: F 343 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7997 (tttm) REVERT: F 349 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.5565 (pmt170) outliers start: 9 outliers final: 2 residues processed: 108 average time/residue: 1.2122 time to fit residues: 134.4232 Evaluate side-chains 101 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 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 = 0.3655 r_free = 0.3655 target = 0.108408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097257 restraints weight = 4915.887| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.92 r_work: 0.3367 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3429 Z= 0.306 Angle : 0.647 7.363 4590 Z= 0.317 Chirality : 0.050 0.137 519 Planarity : 0.003 0.019 582 Dihedral : 4.979 13.286 450 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.07 % Allowed : 18.86 % Favored : 79.07 % 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: -2.18 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.017 0.002 PHE F 346 TYR 0.027 0.003 TYR E 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.383 Fit side-chains REVERT: A 338 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7885 (tt0) REVERT: A 340 LYS cc_start: 0.8468 (mttt) cc_final: 0.8256 (mttm) REVERT: B 311 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8465 (pttm) REVERT: B 340 LYS cc_start: 0.8951 (mttt) cc_final: 0.8684 (mttm) REVERT: E 311 LYS cc_start: 0.8657 (pttt) cc_final: 0.8359 (ptmt) REVERT: E 340 LYS cc_start: 0.8413 (mttt) cc_final: 0.8069 (mtpm) REVERT: E 345 ASP cc_start: 0.8140 (t0) cc_final: 0.7709 (t0) REVERT: F 311 LYS cc_start: 0.8605 (pttt) cc_final: 0.8193 (ptmt) REVERT: F 342 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7846 (mp0) REVERT: F 343 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7883 (tttt) REVERT: F 349 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.5563 (pmt170) REVERT: F 375 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8589 (ttpp) outliers start: 8 outliers final: 3 residues processed: 99 average time/residue: 1.1874 time to fit residues: 120.6954 Evaluate side-chains 100 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.109404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097808 restraints weight = 4615.307| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.83 r_work: 0.3346 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3429 Z= 0.385 Angle : 0.688 7.473 4590 Z= 0.336 Chirality : 0.051 0.139 519 Planarity : 0.003 0.021 582 Dihedral : 5.165 13.894 450 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.81 % Allowed : 19.38 % Favored : 78.81 % 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: -2.28 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.014 0.002 PHE F 346 TYR 0.027 0.004 TYR D 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.483 Fit side-chains REVERT: A 338 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7907 (tt0) REVERT: A 340 LYS cc_start: 0.8515 (mttt) cc_final: 0.8295 (mttm) REVERT: B 311 LYS cc_start: 0.8864 (ttmt) cc_final: 0.8510 (pttm) REVERT: B 340 LYS cc_start: 0.8958 (mttt) cc_final: 0.8706 (mttm) REVERT: E 311 LYS cc_start: 0.8673 (pttt) cc_final: 0.8385 (ptmt) REVERT: E 340 LYS cc_start: 0.8394 (mttt) cc_final: 0.8076 (mtpm) REVERT: E 345 ASP cc_start: 0.8199 (t0) cc_final: 0.7795 (t0) REVERT: F 311 LYS cc_start: 0.8617 (pttt) cc_final: 0.8242 (ptmt) REVERT: F 342 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8014 (mp0) REVERT: F 343 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7924 (tttt) REVERT: F 349 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.5660 (pmt170) outliers start: 7 outliers final: 4 residues processed: 102 average time/residue: 1.2903 time to fit residues: 135.1147 Evaluate side-chains 100 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.111163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.099588 restraints weight = 4447.294| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.81 r_work: 0.3385 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3429 Z= 0.225 Angle : 0.619 8.110 4590 Z= 0.296 Chirality : 0.049 0.120 519 Planarity : 0.002 0.018 582 Dihedral : 4.781 13.582 450 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.33 % Allowed : 18.86 % Favored : 78.81 % 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: -2.25 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.013 0.001 PHE F 346 TYR 0.024 0.002 TYR E 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.376 Fit side-chains REVERT: A 338 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7878 (tt0) REVERT: A 340 LYS cc_start: 0.8496 (mttt) cc_final: 0.8273 (mttm) REVERT: A 379 ARG cc_start: 0.7635 (mtm180) cc_final: 0.7416 (mtp180) REVERT: B 311 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8476 (pttm) REVERT: B 338 GLU cc_start: 0.8573 (tt0) cc_final: 0.8314 (tt0) REVERT: B 340 LYS cc_start: 0.8979 (mttt) cc_final: 0.8722 (mttm) REVERT: E 311 LYS cc_start: 0.8538 (pttt) cc_final: 0.8252 (ptmt) REVERT: E 338 GLU cc_start: 0.8597 (tt0) cc_final: 0.8373 (tt0) REVERT: E 340 LYS cc_start: 0.8334 (mttt) cc_final: 0.7918 (mptt) REVERT: E 345 ASP cc_start: 0.8124 (t0) cc_final: 0.7691 (t0) REVERT: E 349 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7585 (mtp85) REVERT: F 311 LYS cc_start: 0.8517 (pttt) cc_final: 0.8131 (ptmt) REVERT: F 342 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7823 (pm20) REVERT: F 343 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7834 (tttt) outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 1.1777 time to fit residues: 122.1775 Evaluate side-chains 102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 0.0870 chunk 30 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 33 optimal weight: 0.0000 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 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 = 0.3700 r_free = 0.3700 target = 0.112880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101235 restraints weight = 4408.617| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.82 r_work: 0.3419 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3429 Z= 0.184 Angle : 0.586 8.433 4590 Z= 0.279 Chirality : 0.049 0.121 519 Planarity : 0.002 0.018 582 Dihedral : 4.522 13.624 450 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.55 % Allowed : 19.64 % Favored : 78.81 % 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: -2.23 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.013 0.001 PHE F 346 TYR 0.028 0.003 TYR D 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.417 Fit side-chains REVERT: A 338 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7904 (tt0) REVERT: A 340 LYS cc_start: 0.8539 (mttt) cc_final: 0.8325 (mttm) REVERT: B 311 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8462 (pttm) REVERT: C 379 ARG cc_start: 0.7614 (mtm180) cc_final: 0.7362 (mmm160) REVERT: D 345 ASP cc_start: 0.7762 (t70) cc_final: 0.7097 (t70) REVERT: E 311 LYS cc_start: 0.8497 (pttt) cc_final: 0.8234 (ptmt) REVERT: E 340 LYS cc_start: 0.8378 (mttt) cc_final: 0.8072 (mttp) REVERT: E 343 LYS cc_start: 0.8104 (ttmt) cc_final: 0.7225 (mmtt) REVERT: E 345 ASP cc_start: 0.8096 (t0) cc_final: 0.7629 (t70) REVERT: E 349 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7593 (mtp85) REVERT: F 311 LYS cc_start: 0.8492 (pttt) cc_final: 0.8094 (ptmt) REVERT: F 342 GLU cc_start: 0.8604 (mt-10) cc_final: 0.7861 (pm20) REVERT: F 343 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7852 (tttt) outliers start: 6 outliers final: 4 residues processed: 100 average time/residue: 1.1879 time to fit residues: 122.0605 Evaluate side-chains 100 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 349 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 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 = 0.3633 r_free = 0.3633 target = 0.105993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094886 restraints weight = 4984.329| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.88 r_work: 0.3358 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3429 Z= 0.489 Angle : 0.732 7.936 4590 Z= 0.361 Chirality : 0.052 0.146 519 Planarity : 0.003 0.021 582 Dihedral : 5.240 14.890 450 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.81 % Allowed : 19.12 % Favored : 79.07 % 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: -2.37 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.011 0.002 PHE E 346 TYR 0.021 0.004 TYR E 310 ARG 0.004 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.392 Fit side-chains REVERT: A 338 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7844 (tt0) REVERT: A 340 LYS cc_start: 0.8528 (mttt) cc_final: 0.8301 (mttm) REVERT: E 311 LYS cc_start: 0.8670 (pttt) cc_final: 0.8376 (ptmt) REVERT: E 340 LYS cc_start: 0.8383 (mttt) cc_final: 0.8141 (mttp) REVERT: E 345 ASP cc_start: 0.8206 (t0) cc_final: 0.7806 (t0) REVERT: F 311 LYS cc_start: 0.8628 (pttt) cc_final: 0.8227 (ptmt) REVERT: F 342 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8066 (mp0) REVERT: F 343 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7892 (tttt) outliers start: 7 outliers final: 4 residues processed: 97 average time/residue: 1.1151 time to fit residues: 111.2140 Evaluate side-chains 97 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain E residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.109986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098551 restraints weight = 4550.228| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.82 r_work: 0.3353 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3429 Z= 0.307 Angle : 0.656 8.355 4590 Z= 0.317 Chirality : 0.050 0.129 519 Planarity : 0.003 0.020 582 Dihedral : 5.000 14.642 450 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.29 % Allowed : 19.38 % Favored : 79.33 % 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: -2.41 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.010 0.002 PHE F 346 TYR 0.026 0.004 TYR D 310 ARG 0.003 0.000 ARG F 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.419 Fit side-chains REVERT: A 338 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7865 (tt0) REVERT: A 340 LYS cc_start: 0.8540 (mttt) cc_final: 0.8320 (mttm) REVERT: E 311 LYS cc_start: 0.8602 (pttt) cc_final: 0.8325 (ptmt) REVERT: E 340 LYS cc_start: 0.8379 (mttt) cc_final: 0.8005 (mttp) REVERT: E 343 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7313 (mmtt) REVERT: E 345 ASP cc_start: 0.8214 (t0) cc_final: 0.7805 (t0) REVERT: F 311 LYS cc_start: 0.8579 (pttt) cc_final: 0.8174 (ptmt) REVERT: F 342 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8079 (mp0) REVERT: F 343 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7913 (tttt) outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 1.2415 time to fit residues: 131.2221 Evaluate side-chains 103 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain E residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 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 = 0.3637 r_free = 0.3637 target = 0.108440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.096979 restraints weight = 4637.541| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.83 r_work: 0.3333 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3429 Z= 0.396 Angle : 0.698 8.330 4590 Z= 0.341 Chirality : 0.051 0.139 519 Planarity : 0.003 0.020 582 Dihedral : 5.135 14.763 450 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.33 % Allowed : 19.12 % Favored : 78.55 % 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: -2.44 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.009 0.002 PHE F 346 TYR 0.019 0.003 TYR E 310 ARG 0.004 0.001 ARG C 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3712.67 seconds wall clock time: 64 minutes 17.83 seconds (3857.83 seconds total)