Starting phenix.real_space_refine on Fri Aug 22 13:40:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7l_18219/08_2025/8q7l_18219.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7l_18219/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8q7l_18219/08_2025/8q7l_18219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7l_18219/08_2025/8q7l_18219.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q7l_18219/08_2025/8q7l_18219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7l_18219/08_2025/8q7l_18219.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.28, per 1000 atoms: 0.38 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: 0.28 Conformation dependent library (CDL) restraints added in 160.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.16 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: 0.53 Time building geometry restraints manager: 0.40 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: 0.00 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: 5.180 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.180 Find NCS groups from input model: 0.070 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:10.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.730 ------------------------------------------------------------------------------- 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= 0.683 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.002 ARG E 349 TYR 0.056 0.012 TYR E 310 PHE 0.033 0.010 PHE D 346 HIS 0.009 0.003 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.01094 ( 3429) covalent geometry : angle 1.90431 ( 4590) hydrogen bonds : bond 0.08747 ( 73) hydrogen bonds : angle 7.60608 ( 219) *********************** 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 : 0.152 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: 0.7689 (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: 0.6742 time to fit residues: 105.4466 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 : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.117350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.106087 restraints weight = 4546.877| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.87 r_work: 0.3494 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3429 Z= 0.121 Angle : 0.638 5.469 4590 Z= 0.317 Chirality : 0.051 0.134 519 Planarity : 0.003 0.033 582 Dihedral : 5.497 16.097 450 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.81 % Allowed : 13.95 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 349 TYR 0.027 0.003 TYR D 310 PHE 0.009 0.002 PHE D 378 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3429) covalent geometry : angle 0.63801 ( 4590) hydrogen bonds : bond 0.02139 ( 73) hydrogen bonds : angle 5.13115 ( 219) *********************** 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 132 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8032 (tt0) REVERT: A 340 LYS cc_start: 0.8529 (mttt) cc_final: 0.8276 (mttm) REVERT: B 311 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8597 (pttm) REVERT: B 340 LYS cc_start: 0.8813 (mttt) cc_final: 0.8540 (mttm) REVERT: B 369 LYS cc_start: 0.8214 (ttmt) cc_final: 0.8014 (tttt) REVERT: B 372 GLU cc_start: 0.4233 (mm-30) cc_final: 0.2761 (pt0) REVERT: C 311 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8062 (mmtm) REVERT: C 338 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8030 (tt0) REVERT: C 370 LYS cc_start: 0.8916 (tttt) cc_final: 0.8660 (tttm) REVERT: C 375 LYS cc_start: 0.8149 (ptmt) cc_final: 0.7734 (ptpp) REVERT: E 311 LYS cc_start: 0.8586 (pttt) cc_final: 0.8244 (ptmt) REVERT: E 343 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7158 (mmtt) REVERT: E 345 ASP cc_start: 0.8113 (t0) cc_final: 0.7708 (t70) REVERT: F 311 LYS cc_start: 0.8427 (pttt) cc_final: 0.8122 (ptmt) REVERT: F 342 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7910 (mp0) outliers start: 7 outliers final: 2 residues processed: 129 average time/residue: 0.6511 time to fit residues: 85.9965 Evaluate side-chains 103 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 37 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.108789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097361 restraints weight = 4566.843| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.80 r_work: 0.3343 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 3429 Z= 0.349 Angle : 0.807 7.146 4590 Z= 0.404 Chirality : 0.056 0.159 519 Planarity : 0.004 0.025 582 Dihedral : 5.787 17.189 450 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.58 % Allowed : 18.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 349 TYR 0.026 0.005 TYR E 310 PHE 0.011 0.002 PHE A 346 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00819 ( 3429) covalent geometry : angle 0.80693 ( 4590) hydrogen bonds : bond 0.02279 ( 73) hydrogen bonds : angle 4.87361 ( 219) *********************** 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 115 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7977 (tt0) REVERT: A 340 LYS cc_start: 0.8574 (mttt) cc_final: 0.8350 (mttm) REVERT: A 363 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.9036 (t) REVERT: B 311 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8490 (pttm) REVERT: B 338 GLU cc_start: 0.8597 (tt0) cc_final: 0.8290 (tt0) REVERT: B 340 LYS cc_start: 0.8946 (mttt) cc_final: 0.8682 (mttm) REVERT: B 369 LYS cc_start: 0.8312 (ttmt) cc_final: 0.8111 (tttt) REVERT: E 311 LYS cc_start: 0.8795 (pttt) cc_final: 0.8579 (ptmt) REVERT: E 345 ASP cc_start: 0.8236 (t0) cc_final: 0.7886 (t0) REVERT: F 311 LYS cc_start: 0.8624 (pttt) cc_final: 0.8277 (ptmt) REVERT: F 342 GLU cc_start: 0.8508 (mt-10) cc_final: 0.7999 (mp0) REVERT: F 343 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7966 (tttm) REVERT: F 349 ARG cc_start: 0.8361 (mpp80) cc_final: 0.5353 (pmt170) outliers start: 10 outliers final: 5 residues processed: 107 average time/residue: 0.6582 time to fit residues: 72.1053 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 : 0.145 ------------------------------------------------------------------------------- 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 B residue 375 LYS Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS F 307 GLN F 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.109878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.098703 restraints weight = 4735.285| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.83 r_work: 0.3382 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3429 Z= 0.146 Angle : 0.650 7.613 4590 Z= 0.315 Chirality : 0.050 0.136 519 Planarity : 0.003 0.022 582 Dihedral : 5.173 13.662 450 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.33 % Allowed : 17.83 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.030 0.003 TYR E 310 PHE 0.007 0.001 PHE A 346 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3429) covalent geometry : angle 0.64957 ( 4590) hydrogen bonds : bond 0.01805 ( 73) hydrogen bonds : angle 4.53168 ( 219) *********************** 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 118 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.177 Fit side-chains REVERT: A 338 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7919 (tt0) REVERT: A 340 LYS cc_start: 0.8516 (mttt) cc_final: 0.8296 (mttm) REVERT: B 311 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8418 (pttm) REVERT: B 338 GLU cc_start: 0.8588 (tt0) cc_final: 0.8227 (tt0) REVERT: B 340 LYS cc_start: 0.8937 (mttt) cc_final: 0.8629 (mttm) REVERT: B 369 LYS cc_start: 0.8283 (ttmt) cc_final: 0.8076 (tttt) REVERT: C 336 GLN cc_start: 0.8123 (mt0) cc_final: 0.7745 (mp10) REVERT: E 311 LYS cc_start: 0.8594 (pttt) cc_final: 0.8340 (ptmt) REVERT: E 340 LYS cc_start: 0.8413 (mttt) cc_final: 0.8058 (mtpm) REVERT: E 345 ASP cc_start: 0.8161 (t0) cc_final: 0.7707 (t70) REVERT: F 311 LYS cc_start: 0.8601 (pttt) cc_final: 0.8230 (ptmt) REVERT: F 342 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7907 (mp0) REVERT: F 343 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7925 (tttm) REVERT: F 375 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8610 (ttpp) outliers start: 9 outliers final: 3 residues processed: 110 average time/residue: 0.6347 time to fit residues: 71.5209 Evaluate side-chains 105 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 0.0010 chunk 35 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN F 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.110757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.099348 restraints weight = 4468.120| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.79 r_work: 0.3384 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3429 Z= 0.174 Angle : 0.642 7.666 4590 Z= 0.311 Chirality : 0.050 0.127 519 Planarity : 0.003 0.019 582 Dihedral : 5.051 13.623 450 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.58 % Allowed : 18.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.030 0.004 TYR D 310 PHE 0.007 0.001 PHE A 346 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3429) covalent geometry : angle 0.64199 ( 4590) hydrogen bonds : bond 0.01805 ( 73) hydrogen bonds : angle 4.43585 ( 219) *********************** 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 110 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.119 Fit side-chains REVERT: A 338 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7941 (tt0) REVERT: A 340 LYS cc_start: 0.8514 (mttt) cc_final: 0.8303 (mttm) REVERT: B 311 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8466 (pttm) REVERT: B 338 GLU cc_start: 0.8579 (tt0) cc_final: 0.8220 (tt0) REVERT: B 340 LYS cc_start: 0.8939 (mttt) cc_final: 0.8641 (mttm) REVERT: C 336 GLN cc_start: 0.8166 (mt0) cc_final: 0.7856 (mp10) REVERT: C 342 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8354 (pt0) REVERT: E 311 LYS cc_start: 0.8615 (pttt) cc_final: 0.8342 (ptmt) REVERT: E 340 LYS cc_start: 0.8396 (mttt) cc_final: 0.8142 (mttp) REVERT: E 345 ASP cc_start: 0.8180 (t0) cc_final: 0.7767 (t0) REVERT: F 311 LYS cc_start: 0.8621 (pttt) cc_final: 0.8247 (ptmt) REVERT: F 342 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7881 (mp0) REVERT: F 343 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7997 (tttm) REVERT: F 349 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7524 (mtp85) REVERT: F 375 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8622 (ttpp) outliers start: 10 outliers final: 4 residues processed: 102 average time/residue: 0.6548 time to fit residues: 68.3643 Evaluate side-chains 104 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 349 ARG 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 32 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.108617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.097102 restraints weight = 4565.129| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.86 r_work: 0.3341 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 3429 Z= 0.240 Angle : 0.691 7.554 4590 Z= 0.338 Chirality : 0.051 0.137 519 Planarity : 0.003 0.021 582 Dihedral : 5.190 13.682 450 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.36 % Allowed : 17.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.023 0.003 TYR E 310 PHE 0.008 0.002 PHE A 346 HIS 0.004 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 3429) covalent geometry : angle 0.69091 ( 4590) hydrogen bonds : bond 0.01830 ( 73) hydrogen bonds : angle 4.41417 ( 219) *********************** 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 112 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7866 (tt0) REVERT: A 340 LYS cc_start: 0.8523 (mttt) cc_final: 0.8292 (mttm) REVERT: B 311 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8483 (pttm) REVERT: B 338 GLU cc_start: 0.8613 (tt0) cc_final: 0.8407 (tt0) REVERT: B 340 LYS cc_start: 0.8971 (mttt) cc_final: 0.8715 (mttm) REVERT: C 336 GLN cc_start: 0.8210 (mt0) cc_final: 0.7880 (mp10) REVERT: E 311 LYS cc_start: 0.8628 (pttt) cc_final: 0.8324 (ptmt) REVERT: E 340 LYS cc_start: 0.8435 (mttt) cc_final: 0.8156 (mttp) REVERT: E 345 ASP cc_start: 0.8197 (t0) cc_final: 0.7788 (t0) REVERT: E 349 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7601 (mtp85) REVERT: F 311 LYS cc_start: 0.8610 (pttt) cc_final: 0.8220 (ptmt) REVERT: F 342 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7985 (mp0) REVERT: F 343 LYS cc_start: 0.8275 (ttmt) cc_final: 0.8040 (tttm) REVERT: F 349 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7581 (mtp85) outliers start: 13 outliers final: 3 residues processed: 102 average time/residue: 0.6758 time to fit residues: 70.5054 Evaluate side-chains 101 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain F residue 349 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 0.0370 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.113986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.102382 restraints weight = 4494.748| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.83 r_work: 0.3427 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3429 Z= 0.102 Angle : 0.589 8.073 4590 Z= 0.278 Chirality : 0.049 0.121 519 Planarity : 0.002 0.017 582 Dihedral : 4.575 13.858 450 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.29 % Allowed : 19.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.029 0.003 TYR D 310 PHE 0.005 0.001 PHE D 346 HIS 0.002 0.000 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 3429) covalent geometry : angle 0.58888 ( 4590) hydrogen bonds : bond 0.01452 ( 73) hydrogen bonds : angle 4.18273 ( 219) *********************** 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 109 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.153 Fit side-chains REVERT: A 338 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7899 (tt0) REVERT: A 340 LYS cc_start: 0.8510 (mttt) cc_final: 0.8294 (mttm) REVERT: B 311 LYS cc_start: 0.8763 (ttmt) cc_final: 0.8417 (pttm) REVERT: B 338 GLU cc_start: 0.8581 (tt0) cc_final: 0.8267 (tt0) REVERT: B 340 LYS cc_start: 0.8987 (mttt) cc_final: 0.8734 (mttm) REVERT: C 336 GLN cc_start: 0.8200 (mt0) cc_final: 0.7907 (mp10) REVERT: C 358 ASP cc_start: 0.7633 (m-30) cc_final: 0.7406 (m-30) REVERT: D 345 ASP cc_start: 0.7736 (t70) cc_final: 0.6995 (t70) REVERT: E 340 LYS cc_start: 0.8370 (mttt) cc_final: 0.8148 (mttp) REVERT: E 343 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7202 (mmtt) REVERT: E 345 ASP cc_start: 0.8092 (t0) cc_final: 0.7579 (t70) REVERT: E 349 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7606 (mtp85) REVERT: F 311 LYS cc_start: 0.8510 (pttt) cc_final: 0.8133 (ptmt) REVERT: F 342 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7845 (pm20) REVERT: F 343 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7815 (tttt) outliers start: 5 outliers final: 2 residues processed: 105 average time/residue: 0.6411 time to fit residues: 68.9620 Evaluate side-chains 98 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain E residue 349 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.110250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098845 restraints weight = 4559.233| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.83 r_work: 0.3354 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3429 Z= 0.226 Angle : 0.670 7.999 4590 Z= 0.327 Chirality : 0.050 0.133 519 Planarity : 0.003 0.020 582 Dihedral : 4.956 13.567 450 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.03 % Allowed : 21.71 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.015 0.003 TYR A 310 PHE 0.018 0.002 PHE F 346 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 3429) covalent geometry : angle 0.67044 ( 4590) hydrogen bonds : bond 0.01643 ( 73) hydrogen bonds : angle 4.23609 ( 219) *********************** 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: 4 poor density : 100 time to evaluate : 0.145 Fit side-chains REVERT: A 338 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7875 (tt0) REVERT: A 340 LYS cc_start: 0.8560 (mttt) cc_final: 0.8339 (mttm) REVERT: B 311 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8521 (pttm) REVERT: C 336 GLN cc_start: 0.8249 (mt0) cc_final: 0.7960 (mp10) REVERT: E 311 LYS cc_start: 0.8558 (pttt) cc_final: 0.8341 (ptmt) REVERT: E 340 LYS cc_start: 0.8452 (mttt) cc_final: 0.8248 (mttp) REVERT: E 343 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7278 (mmtt) REVERT: E 345 ASP cc_start: 0.8203 (t0) cc_final: 0.7777 (t0) REVERT: E 349 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7616 (mtp85) REVERT: F 311 LYS cc_start: 0.8601 (pttt) cc_final: 0.8221 (ptmt) REVERT: F 342 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8069 (mp0) REVERT: F 343 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7892 (tttt) outliers start: 4 outliers final: 2 residues processed: 102 average time/residue: 0.6528 time to fit residues: 68.0870 Evaluate side-chains 100 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 356 SER 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 0 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3639 r_free = 0.3639 target = 0.108369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097359 restraints weight = 4834.320| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.82 r_work: 0.3374 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.4511 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= 0.197 Angle : 0.649 7.827 4590 Z= 0.314 Chirality : 0.050 0.128 519 Planarity : 0.003 0.019 582 Dihedral : 4.924 13.776 450 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.03 % Allowed : 21.96 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.028 0.004 TYR D 310 PHE 0.018 0.002 PHE F 346 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 3429) covalent geometry : angle 0.64853 ( 4590) hydrogen bonds : bond 0.01599 ( 73) hydrogen bonds : angle 4.21488 ( 219) *********************** 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 106 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.154 Fit side-chains REVERT: A 338 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7846 (tt0) REVERT: A 340 LYS cc_start: 0.8528 (mttt) cc_final: 0.8294 (mttm) REVERT: C 336 GLN cc_start: 0.8236 (mt0) cc_final: 0.7944 (mp10) REVERT: E 340 LYS cc_start: 0.8465 (mttt) cc_final: 0.8092 (mttp) REVERT: E 343 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7291 (mmtt) REVERT: E 345 ASP cc_start: 0.8202 (t0) cc_final: 0.7771 (t0) REVERT: E 349 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7577 (mtp85) REVERT: F 311 LYS cc_start: 0.8524 (pttt) cc_final: 0.8138 (ptmt) REVERT: F 342 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8054 (mp0) REVERT: F 343 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7891 (tttt) outliers start: 4 outliers final: 3 residues processed: 102 average time/residue: 0.5929 time to fit residues: 61.9555 Evaluate side-chains 106 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 33 optimal weight: 0.0370 chunk 24 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.108366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097371 restraints weight = 4943.850| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.86 r_work: 0.3367 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.4631 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= 0.199 Angle : 0.665 7.995 4590 Z= 0.324 Chirality : 0.050 0.130 519 Planarity : 0.003 0.019 582 Dihedral : 4.948 14.087 450 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.29 % Allowed : 21.96 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 349 TYR 0.020 0.003 TYR E 310 PHE 0.017 0.002 PHE F 346 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 3429) covalent geometry : angle 0.66500 ( 4590) hydrogen bonds : bond 0.01526 ( 73) hydrogen bonds : angle 4.18424 ( 219) ********************** 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 108 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.095 Fit side-chains REVERT: A 338 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7844 (tt0) REVERT: A 340 LYS cc_start: 0.8534 (mttt) cc_final: 0.8298 (mttm) REVERT: C 336 GLN cc_start: 0.8235 (mt0) cc_final: 0.7932 (mp10) REVERT: E 340 LYS cc_start: 0.8520 (mttt) cc_final: 0.8157 (mttp) REVERT: E 343 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7318 (mmtt) REVERT: E 345 ASP cc_start: 0.8211 (t0) cc_final: 0.7718 (t70) REVERT: E 349 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7569 (mtp85) REVERT: F 311 LYS cc_start: 0.8555 (pttt) cc_final: 0.8165 (ptmt) REVERT: F 342 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8048 (mp0) REVERT: F 343 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7892 (tttt) outliers start: 5 outliers final: 4 residues processed: 104 average time/residue: 0.6400 time to fit residues: 68.1425 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 : 0.120 ------------------------------------------------------------------------------- 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 D residue 311 LYS Chi-restraints excluded: chain E residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097028 restraints weight = 5000.603| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.88 r_work: 0.3360 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.4614 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= 0.201 Angle : 0.672 8.076 4590 Z= 0.326 Chirality : 0.050 0.131 519 Planarity : 0.003 0.019 582 Dihedral : 4.951 15.290 450 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.03 % Allowed : 22.48 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 349 TYR 0.029 0.004 TYR D 310 PHE 0.017 0.002 PHE F 346 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 3429) covalent geometry : angle 0.67209 ( 4590) hydrogen bonds : bond 0.01524 ( 73) hydrogen bonds : angle 4.18506 ( 219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1999.93 seconds wall clock time: 34 minutes 56.15 seconds (2096.15 seconds total)