Starting phenix.real_space_refine on Tue Feb 11 00:45:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7l_18219/02_2025/8q7l_18219.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7l_18219/02_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_18219/02_2025/8q7l_18219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7l_18219/02_2025/8q7l_18219.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7l_18219/02_2025/8q7l_18219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7l_18219/02_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-5592/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: 3.63, per 1000 atoms: 1.08 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: 0.82 Conformation dependent library (CDL) restraints added in 434.3 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: 0.57 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: 0.81 Time building geometry restraints manager: 0.99 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.940 Find NCS groups from input model: 0.150 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.610 ------------------------------------------------------------------------------- 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 : 0.429 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: 1.3491 time to fit residues: 211.1093 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 : 0.437 ------------------------------------------------------------------------------- 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 = 0.105519 restraints weight = 4398.037| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.79 r_work: 0.3469 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 : 0.396 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: 0.8287 (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: 0.8546 (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: 0.8204 (t0) cc_final: 0.7820 (t70) REVERT: F 311 LYS cc_start: 0.8431 (pttt) cc_final: 0.8140 (ptmt) REVERT: F 342 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7943 (mp0) REVERT: F 349 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.8005 (mtm180) outliers start: 7 outliers final: 2 residues processed: 123 average time/residue: 1.2454 time to fit residues: 157.0223 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 : 0.432 ------------------------------------------------------------------------------- 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: 4.9990 chunk 39 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.108694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097643 restraints weight = 4932.749| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.86 r_work: 0.3385 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3429 Z= 0.409 Angle : 0.734 6.715 4590 Z= 0.365 Chirality : 0.053 0.147 519 Planarity : 0.003 0.023 582 Dihedral : 5.528 16.206 450 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.07 % Allowed : 18.35 % Favored : 79.59 % 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: -2.03 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.009 0.002 PHE B 378 TYR 0.013 0.003 TYR C 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 119 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7973 (tt0) REVERT: B 311 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8480 (pttm) REVERT: B 340 LYS cc_start: 0.8937 (mttt) cc_final: 0.8657 (mttm) REVERT: C 311 LYS cc_start: 0.8877 (ttmt) cc_final: 0.8207 (mmtm) REVERT: C 370 LYS cc_start: 0.8945 (tttt) cc_final: 0.8566 (tttm) REVERT: C 375 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7743 (ptpp) REVERT: E 311 LYS cc_start: 0.8759 (pttt) cc_final: 0.8378 (ptmt) REVERT: E 345 ASP cc_start: 0.8206 (t0) cc_final: 0.7810 (t0) REVERT: E 370 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8115 (tmtt) REVERT: F 311 LYS cc_start: 0.8557 (pttt) cc_final: 0.8186 (ptmt) REVERT: F 342 GLU cc_start: 0.8505 (mt-10) cc_final: 0.7910 (mp0) REVERT: F 343 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7942 (tttm) REVERT: F 349 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.8130 (mtm180) outliers start: 8 outliers final: 5 residues processed: 114 average time/residue: 1.3708 time to fit residues: 160.0604 Evaluate side-chains 102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.112799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101201 restraints weight = 4489.375| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.84 r_work: 0.3421 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3429 Z= 0.183 Angle : 0.604 7.747 4590 Z= 0.291 Chirality : 0.049 0.127 519 Planarity : 0.003 0.020 582 Dihedral : 4.876 13.217 450 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.07 % Allowed : 19.38 % 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: -2.13 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.008 0.001 PHE B 378 TYR 0.030 0.003 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 114 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.431 Fit side-chains REVERT: A 338 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7960 (tt0) REVERT: B 311 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8473 (pttm) REVERT: B 338 GLU cc_start: 0.8524 (tt0) cc_final: 0.8200 (tt0) REVERT: B 340 LYS cc_start: 0.8908 (mttt) cc_final: 0.8606 (mttm) REVERT: C 358 ASP cc_start: 0.7464 (m-30) cc_final: 0.7221 (m-30) REVERT: E 311 LYS cc_start: 0.8595 (pttt) cc_final: 0.8225 (ptmt) REVERT: E 343 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7057 (mmtt) REVERT: E 345 ASP cc_start: 0.8129 (t0) cc_final: 0.7631 (t70) REVERT: F 311 LYS cc_start: 0.8589 (pttt) cc_final: 0.8193 (ptmt) REVERT: F 342 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7853 (mp0) REVERT: F 343 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7967 (tttm) REVERT: F 349 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.5550 (pmt170) outliers start: 8 outliers final: 3 residues processed: 107 average time/residue: 1.2174 time to fit residues: 133.8170 Evaluate side-chains 99 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B 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: 2.9990 chunk 22 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.109703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098542 restraints weight = 4857.235| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.88 r_work: 0.3383 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3429 Z= 0.271 Angle : 0.639 7.287 4590 Z= 0.309 Chirality : 0.050 0.129 519 Planarity : 0.003 0.018 582 Dihedral : 4.890 13.157 450 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.07 % Allowed : 18.60 % 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: -2.17 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.016 0.002 PHE F 346 TYR 0.027 0.004 TYR E 310 ARG 0.003 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 110 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.409 Fit side-chains REVERT: A 338 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7946 (tt0) REVERT: B 311 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8482 (pttm) REVERT: B 338 GLU cc_start: 0.8585 (tt0) cc_final: 0.8246 (tt0) REVERT: B 340 LYS cc_start: 0.8947 (mttt) cc_final: 0.8637 (mttm) REVERT: C 358 ASP cc_start: 0.7456 (m-30) cc_final: 0.7183 (m-30) REVERT: E 311 LYS cc_start: 0.8614 (pttt) cc_final: 0.8324 (ptmt) REVERT: E 340 LYS cc_start: 0.8411 (mttt) cc_final: 0.8086 (mtpm) REVERT: E 343 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7141 (mmtt) REVERT: E 345 ASP cc_start: 0.8164 (t0) cc_final: 0.7667 (t70) REVERT: F 311 LYS cc_start: 0.8598 (pttt) cc_final: 0.8205 (ptmt) REVERT: F 342 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7872 (mp0) REVERT: F 343 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7945 (tttt) REVERT: F 349 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.5588 (pmt170) REVERT: F 372 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8394 (mt-10) outliers start: 8 outliers final: 4 residues processed: 104 average time/residue: 1.2172 time to fit residues: 130.0792 Evaluate side-chains 101 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 341 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.109790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.098155 restraints weight = 4602.343| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.83 r_work: 0.3350 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3429 Z= 0.354 Angle : 0.675 7.514 4590 Z= 0.328 Chirality : 0.051 0.137 519 Planarity : 0.003 0.020 582 Dihedral : 5.079 13.458 450 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.81 % Allowed : 19.90 % Favored : 78.29 % 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: -2.24 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.013 0.002 PHE F 346 TYR 0.028 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 103 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.441 Fit side-chains REVERT: A 338 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7921 (tt0) REVERT: B 311 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8519 (pttm) REVERT: B 338 GLU cc_start: 0.8577 (tt0) cc_final: 0.8330 (tt0) REVERT: B 340 LYS cc_start: 0.8959 (mttt) cc_final: 0.8711 (mttm) REVERT: E 311 LYS cc_start: 0.8655 (pttt) cc_final: 0.8363 (ptmt) REVERT: E 340 LYS cc_start: 0.8366 (mttt) cc_final: 0.8050 (mtpm) REVERT: E 345 ASP cc_start: 0.8203 (t0) cc_final: 0.7782 (t0) REVERT: E 349 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7634 (mtp85) REVERT: F 311 LYS cc_start: 0.8628 (pttt) cc_final: 0.8252 (ptmt) REVERT: F 342 GLU cc_start: 0.8583 (mt-10) cc_final: 0.7963 (mp0) REVERT: F 343 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7932 (tttt) REVERT: F 349 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.5656 (pmt170) outliers start: 7 outliers final: 4 residues processed: 98 average time/residue: 1.2389 time to fit residues: 124.6800 Evaluate side-chains 98 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 349 ARG 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: 0.3980 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 0.0040 chunk 1 optimal weight: 3.9990 overall best weight: 2.8798 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.109572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098158 restraints weight = 4634.733| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.86 r_work: 0.3358 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: 0.8781 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3429 Z= 0.294 Angle : 0.650 7.855 4590 Z= 0.313 Chirality : 0.050 0.126 519 Planarity : 0.003 0.019 582 Dihedral : 4.968 13.709 450 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.07 % Allowed : 19.12 % 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: -2.26 (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 0.012 0.001 PHE F 346 TYR 0.023 0.004 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 103 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.396 Fit side-chains REVERT: A 338 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7874 (tt0) REVERT: A 379 ARG cc_start: 0.7638 (mtm180) cc_final: 0.7407 (mtp180) REVERT: B 311 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8496 (pttm) REVERT: E 311 LYS cc_start: 0.8610 (pttt) cc_final: 0.8327 (ptmt) REVERT: E 345 ASP cc_start: 0.8174 (t0) cc_final: 0.7743 (t0) REVERT: E 349 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7579 (mtp85) REVERT: F 311 LYS cc_start: 0.8556 (pttt) cc_final: 0.8165 (ptmt) REVERT: F 342 GLU cc_start: 0.8622 (mt-10) cc_final: 0.7977 (mp0) REVERT: F 343 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7842 (tttt) REVERT: F 349 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.5605 (pmt170) outliers start: 8 outliers final: 5 residues processed: 96 average time/residue: 1.2180 time to fit residues: 120.2501 Evaluate side-chains 98 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.110753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099202 restraints weight = 4668.714| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.87 r_work: 0.3391 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3429 Z= 0.193 Angle : 0.596 7.965 4590 Z= 0.285 Chirality : 0.049 0.121 519 Planarity : 0.002 0.018 582 Dihedral : 4.690 13.504 450 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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 0.003 0.001 HIS C 362 PHE 0.011 0.001 PHE F 346 TYR 0.028 0.002 TYR D 310 ARG 0.002 0.000 ARG F 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 96 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.431 Fit side-chains REVERT: A 338 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7863 (tt0) REVERT: D 345 ASP cc_start: 0.7696 (t70) cc_final: 0.7034 (t70) REVERT: E 311 LYS cc_start: 0.8521 (pttt) cc_final: 0.8242 (ptmt) REVERT: E 340 LYS cc_start: 0.8251 (mttp) cc_final: 0.7955 (mmtp) REVERT: E 343 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7199 (mmtt) REVERT: E 345 ASP cc_start: 0.8103 (t0) cc_final: 0.7665 (t0) REVERT: E 349 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7579 (mtp85) REVERT: F 311 LYS cc_start: 0.8493 (pttt) cc_final: 0.8081 (ptmt) REVERT: F 342 GLU cc_start: 0.8606 (mt-10) cc_final: 0.7851 (pm20) REVERT: F 343 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7777 (tttt) REVERT: F 349 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.5522 (pmt170) outliers start: 6 outliers final: 4 residues processed: 92 average time/residue: 1.2009 time to fit residues: 113.6615 Evaluate side-chains 93 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 2 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.109421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.097781 restraints weight = 4489.445| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.82 r_work: 0.3341 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 3429 Z= 0.445 Angle : 0.697 7.965 4590 Z= 0.342 Chirality : 0.051 0.140 519 Planarity : 0.003 0.020 582 Dihedral : 5.099 14.122 450 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.81 % Allowed : 19.90 % Favored : 78.29 % 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: -2.33 (0.33), 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 HIS 0.004 0.001 HIS C 362 PHE 0.010 0.002 PHE E 346 TYR 0.020 0.004 TYR F 310 ARG 0.002 0.000 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 103 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.452 Fit side-chains REVERT: A 338 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7882 (tt0) REVERT: E 311 LYS cc_start: 0.8628 (pttt) cc_final: 0.8336 (ptmt) REVERT: E 340 LYS cc_start: 0.8389 (mttp) cc_final: 0.8093 (mmtp) REVERT: E 343 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7294 (mmtt) REVERT: E 345 ASP cc_start: 0.8218 (t0) cc_final: 0.7792 (t0) REVERT: E 349 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7619 (mtp85) REVERT: F 311 LYS cc_start: 0.8614 (pttt) cc_final: 0.8236 (ptmt) REVERT: F 342 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8095 (mp0) REVERT: F 349 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.5591 (pmt170) outliers start: 7 outliers final: 4 residues processed: 98 average time/residue: 1.2942 time to fit residues: 130.1987 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 : 0.408 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.110937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.099318 restraints weight = 4510.531| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.84 r_work: 0.3364 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3429 Z= 0.274 Angle : 0.638 8.146 4590 Z= 0.307 Chirality : 0.049 0.124 519 Planarity : 0.003 0.019 582 Dihedral : 4.938 14.071 450 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.29 % Allowed : 20.16 % 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: -2.35 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.011 0.001 PHE F 346 TYR 0.027 0.003 TYR D 310 ARG 0.002 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 102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.456 Fit side-chains REVERT: A 338 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7887 (tt0) REVERT: E 311 LYS cc_start: 0.8586 (pttt) cc_final: 0.8297 (ptmt) REVERT: E 340 LYS cc_start: 0.8348 (mttp) cc_final: 0.8049 (mmtp) REVERT: E 343 LYS cc_start: 0.8153 (ttmt) cc_final: 0.7328 (mmtt) REVERT: E 345 ASP cc_start: 0.8207 (t0) cc_final: 0.7778 (t0) REVERT: E 349 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7588 (mtp85) REVERT: F 311 LYS cc_start: 0.8557 (pttt) cc_final: 0.8160 (ptmt) REVERT: F 342 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8089 (mp0) REVERT: F 343 LYS cc_start: 0.8586 (tttm) cc_final: 0.8361 (tttt) REVERT: F 349 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.5610 (pmt170) outliers start: 5 outliers final: 4 residues processed: 98 average time/residue: 1.2633 time to fit residues: 127.0934 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 : 0.417 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 6.9990 chunk 11 optimal weight: 0.0070 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.108486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.096983 restraints weight = 4585.283| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.83 r_work: 0.3328 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3429 Z= 0.428 Angle : 0.707 8.148 4590 Z= 0.346 Chirality : 0.051 0.140 519 Planarity : 0.003 0.021 582 Dihedral : 5.202 14.933 450 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.81 % Allowed : 20.41 % Favored : 77.78 % 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: -2.43 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (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 E 346 TYR 0.020 0.004 TYR F 310 ARG 0.002 0.000 ARG F 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3707.79 seconds wall clock time: 65 minutes 56.27 seconds (3956.27 seconds total)