Starting phenix.real_space_refine on Fri Apr 5 15:19:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7l_18219/04_2024/8q7l_18219.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7l_18219/04_2024/8q7l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7l_18219/04_2024/8q7l_18219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7l_18219/04_2024/8q7l_18219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7l_18219/04_2024/8q7l_18219.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7l_18219/04_2024/8q7l_18219.pdb" } 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 Residue "A GLU 338": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 2.25, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 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: 1.10 Conformation dependent library (CDL) restraints added in 459.5 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 54.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 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: 0.78 Time building geometry restraints manager: 1.19 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: 101.91 - 107.45: 212 107.45 - 112.99: 1685 112.99 - 118.53: 864 118.53 - 124.07: 1558 124.07 - 129.61: 271 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 2.520 nonbonded pdb=" NZ LYS C 347 " pdb=" O GLY E 333 " model vdw 2.250 2.520 nonbonded pdb=" O LYS B 347 " pdb=" NZ LYS F 331 " model vdw 2.276 2.520 nonbonded pdb=" O LYS A 347 " pdb=" NZ LYS D 331 " model vdw 2.328 2.520 nonbonded pdb=" NZ LYS A 343 " pdb=" OE1 GLU D 338 " model vdw 2.385 2.520 ... (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 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: 3.280 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: 10.440 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.320 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.820 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.420 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: 1.3043 time to fit residues: 204.3142 Evaluate side-chains 111 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 F 330 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3105 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= 0.179 Angle : 0.626 5.246 4590 Z= 0.312 Chirality : 0.051 0.133 519 Planarity : 0.003 0.029 582 Dihedral : 5.513 16.023 450 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.07 % Allowed : 13.18 % Favored : 84.75 % 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: -1.83 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.010 0.002 PHE D 378 TYR 0.026 0.003 TYR D 310 ARG 0.005 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 131 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 SER cc_start: 0.8746 (m) cc_final: 0.8490 (t) REVERT: A 338 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7059 (tt0) REVERT: A 340 LYS cc_start: 0.7708 (mttt) cc_final: 0.7279 (mttm) REVERT: A 349 ARG cc_start: 0.7891 (mtt180) cc_final: 0.7612 (mtt-85) REVERT: B 311 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8255 (pttm) REVERT: B 340 LYS cc_start: 0.8371 (mttt) cc_final: 0.7852 (mttm) REVERT: B 369 LYS cc_start: 0.7824 (ttmt) cc_final: 0.7427 (tttt) REVERT: B 372 GLU cc_start: 0.2984 (mm-30) cc_final: 0.1935 (pt0) REVERT: C 311 LYS cc_start: 0.8493 (ttmt) cc_final: 0.7669 (mmtm) REVERT: C 338 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7132 (tt0) REVERT: C 369 LYS cc_start: 0.7661 (ttmt) cc_final: 0.7328 (ttmm) REVERT: C 370 LYS cc_start: 0.8579 (tttt) cc_final: 0.8163 (tttm) REVERT: C 375 LYS cc_start: 0.7717 (ptmt) cc_final: 0.7073 (ptpp) REVERT: E 311 LYS cc_start: 0.8392 (pttt) cc_final: 0.7838 (ptmt) REVERT: E 322 CYS cc_start: 0.8244 (p) cc_final: 0.7732 (m) REVERT: E 343 LYS cc_start: 0.7797 (ttmt) cc_final: 0.6978 (mmtt) REVERT: E 345 ASP cc_start: 0.7790 (t0) cc_final: 0.7331 (t70) REVERT: E 375 LYS cc_start: 0.8113 (tttt) cc_final: 0.7813 (ttpp) REVERT: F 311 LYS cc_start: 0.8052 (pttt) cc_final: 0.7599 (ptmt) REVERT: F 342 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7584 (mp0) REVERT: F 349 ARG cc_start: 0.7454 (mtm-85) cc_final: 0.7190 (mtm180) outliers start: 8 outliers final: 2 residues processed: 126 average time/residue: 1.2472 time to fit residues: 161.1055 Evaluate side-chains 106 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 31 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 37 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- 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 F 368 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3429 Z= 0.401 Angle : 0.737 6.843 4590 Z= 0.367 Chirality : 0.053 0.148 519 Planarity : 0.003 0.023 582 Dihedral : 5.525 15.912 450 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.33 % Allowed : 18.09 % 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: -2.02 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.010 0.002 PHE A 346 TYR 0.025 0.004 TYR E 310 ARG 0.003 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 124 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8166 (mtpt) REVERT: A 338 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6966 (tt0) REVERT: A 340 LYS cc_start: 0.7699 (mttt) cc_final: 0.7308 (mttm) REVERT: A 349 ARG cc_start: 0.7952 (mtt180) cc_final: 0.7692 (mtt-85) REVERT: B 311 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8144 (pttm) REVERT: B 338 GLU cc_start: 0.8252 (tt0) cc_final: 0.7676 (tt0) REVERT: B 340 LYS cc_start: 0.8448 (mttt) cc_final: 0.7936 (mttm) REVERT: B 369 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7506 (tttt) REVERT: C 311 LYS cc_start: 0.8591 (ttmt) cc_final: 0.7733 (mmtm) REVERT: C 336 GLN cc_start: 0.7136 (tt0) cc_final: 0.6676 (mp-120) REVERT: C 369 LYS cc_start: 0.7690 (ttmt) cc_final: 0.7376 (ttmm) REVERT: C 370 LYS cc_start: 0.8614 (tttt) cc_final: 0.8065 (tttm) REVERT: C 375 LYS cc_start: 0.7706 (ptmt) cc_final: 0.6988 (ptpp) REVERT: E 311 LYS cc_start: 0.8468 (pttt) cc_final: 0.7954 (ptmt) REVERT: E 345 ASP cc_start: 0.7804 (t0) cc_final: 0.7369 (t0) REVERT: F 311 LYS cc_start: 0.8227 (pttt) cc_final: 0.7680 (ptmt) REVERT: F 342 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7600 (mp0) REVERT: F 343 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7705 (tttm) REVERT: F 349 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7393 (mtm180) outliers start: 9 outliers final: 5 residues processed: 119 average time/residue: 1.2851 time to fit residues: 156.7827 Evaluate side-chains 109 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 320 SER 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 4 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3429 Z= 0.340 Angle : 0.674 7.006 4590 Z= 0.331 Chirality : 0.051 0.137 519 Planarity : 0.003 0.022 582 Dihedral : 5.285 14.127 450 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.84 % Allowed : 18.60 % 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: -2.20 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.008 0.002 PHE A 346 TYR 0.031 0.004 TYR E 310 ARG 0.003 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.434 Fit side-chains REVERT: A 338 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6943 (tt0) REVERT: A 340 LYS cc_start: 0.7677 (mttt) cc_final: 0.7303 (mttm) REVERT: A 349 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7680 (mtt-85) REVERT: B 311 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8148 (pttm) REVERT: B 338 GLU cc_start: 0.8239 (tt0) cc_final: 0.7675 (tt0) REVERT: B 340 LYS cc_start: 0.8453 (mttt) cc_final: 0.7946 (mttm) REVERT: B 369 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7518 (tttt) REVERT: C 311 LYS cc_start: 0.8583 (ttmt) cc_final: 0.7743 (mmtm) REVERT: C 336 GLN cc_start: 0.7140 (tt0) cc_final: 0.6648 (mp-120) REVERT: C 342 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: C 369 LYS cc_start: 0.7678 (ttmt) cc_final: 0.7350 (ttmm) REVERT: C 370 LYS cc_start: 0.8612 (tttt) cc_final: 0.8094 (tttm) REVERT: C 375 LYS cc_start: 0.7733 (ptmt) cc_final: 0.7349 (ptpp) REVERT: E 311 LYS cc_start: 0.8440 (pttt) cc_final: 0.7949 (ptmt) REVERT: E 345 ASP cc_start: 0.7823 (t0) cc_final: 0.7369 (t0) REVERT: F 311 LYS cc_start: 0.8287 (pttt) cc_final: 0.7736 (ptmt) REVERT: F 342 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7628 (mp0) REVERT: F 343 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7708 (tttm) REVERT: F 349 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7391 (mtm180) outliers start: 11 outliers final: 6 residues processed: 107 average time/residue: 1.3067 time to fit residues: 143.2219 Evaluate side-chains 107 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU 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 D residue 320 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4136 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= 0.276 Angle : 0.644 7.197 4590 Z= 0.311 Chirality : 0.050 0.128 519 Planarity : 0.003 0.025 582 Dihedral : 5.041 13.711 450 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.81 % Allowed : 19.12 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.008 0.001 PHE A 346 TYR 0.023 0.003 TYR F 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 114 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.383 Fit side-chains REVERT: A 311 LYS cc_start: 0.8305 (ttmt) cc_final: 0.8049 (mtpt) REVERT: A 338 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6904 (tt0) REVERT: A 340 LYS cc_start: 0.7616 (mttt) cc_final: 0.7245 (mttm) REVERT: A 349 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7691 (mtt-85) REVERT: B 311 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8098 (pttm) REVERT: B 340 LYS cc_start: 0.8456 (mttt) cc_final: 0.8018 (mttm) REVERT: B 369 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7547 (tttt) REVERT: C 311 LYS cc_start: 0.8599 (ttmt) cc_final: 0.7722 (mmtm) REVERT: C 336 GLN cc_start: 0.7158 (tt0) cc_final: 0.6665 (mp-120) REVERT: C 369 LYS cc_start: 0.7676 (ttmt) cc_final: 0.7325 (ttmm) REVERT: C 370 LYS cc_start: 0.8607 (tttt) cc_final: 0.8157 (tttm) REVERT: C 375 LYS cc_start: 0.7688 (ptmt) cc_final: 0.7299 (ptpp) REVERT: E 311 LYS cc_start: 0.8383 (pttt) cc_final: 0.8036 (ptmt) REVERT: E 340 LYS cc_start: 0.7967 (mttt) cc_final: 0.7598 (mtpm) REVERT: E 345 ASP cc_start: 0.7825 (t0) cc_final: 0.7343 (t0) REVERT: E 349 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6944 (mtp85) REVERT: F 311 LYS cc_start: 0.8257 (pttt) cc_final: 0.7698 (ptmt) REVERT: F 342 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7645 (mp0) REVERT: F 343 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7741 (tttm) REVERT: F 349 ARG cc_start: 0.7665 (mtm-85) cc_final: 0.5764 (pmt170) outliers start: 7 outliers final: 3 residues processed: 108 average time/residue: 1.3102 time to fit residues: 144.9704 Evaluate side-chains 106 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 349 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3429 Z= 0.226 Angle : 0.612 7.560 4590 Z= 0.293 Chirality : 0.049 0.121 519 Planarity : 0.003 0.029 582 Dihedral : 4.779 13.614 450 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -2.24 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.006 0.001 PHE A 346 TYR 0.028 0.003 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 114 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.435 Fit side-chains REVERT: A 338 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6899 (tt0) REVERT: A 340 LYS cc_start: 0.7620 (mttt) cc_final: 0.7227 (mttm) REVERT: A 349 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7684 (mtt-85) REVERT: B 311 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8053 (pttm) REVERT: B 338 GLU cc_start: 0.8179 (tt0) cc_final: 0.7765 (tt0) REVERT: B 340 LYS cc_start: 0.8511 (mttt) cc_final: 0.8044 (mttm) REVERT: B 369 LYS cc_start: 0.7911 (ttmt) cc_final: 0.7518 (tttt) REVERT: C 311 LYS cc_start: 0.8583 (ttmt) cc_final: 0.7696 (mmtm) REVERT: C 369 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7237 (ttmm) REVERT: C 370 LYS cc_start: 0.8606 (tttt) cc_final: 0.8172 (tttm) REVERT: C 375 LYS cc_start: 0.7631 (ptmt) cc_final: 0.7407 (ptpp) REVERT: D 345 ASP cc_start: 0.7396 (t70) cc_final: 0.6682 (t70) REVERT: E 311 LYS cc_start: 0.8326 (pttt) cc_final: 0.7992 (ptmt) REVERT: E 340 LYS cc_start: 0.7905 (mttt) cc_final: 0.7542 (mtpm) REVERT: E 345 ASP cc_start: 0.7818 (t0) cc_final: 0.7347 (t0) REVERT: E 349 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6961 (mtp85) REVERT: F 311 LYS cc_start: 0.8202 (pttt) cc_final: 0.7652 (ptmt) REVERT: F 342 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7494 (pm20) REVERT: F 343 LYS cc_start: 0.8016 (ttmt) cc_final: 0.7605 (tttt) REVERT: F 349 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.5777 (pmt170) outliers start: 8 outliers final: 4 residues processed: 109 average time/residue: 1.2995 time to fit residues: 145.0718 Evaluate side-chains 107 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3429 Z= 0.215 Angle : 0.616 8.051 4590 Z= 0.293 Chirality : 0.049 0.120 519 Planarity : 0.003 0.035 582 Dihedral : 4.672 13.301 450 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.29 % Allowed : 20.41 % 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: -2.25 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.019 0.001 PHE F 346 TYR 0.023 0.002 TYR F 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 111 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.428 Fit side-chains REVERT: A 338 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6907 (tt0) REVERT: A 340 LYS cc_start: 0.7603 (mttt) cc_final: 0.7209 (mttm) REVERT: A 349 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7676 (mtt-85) REVERT: A 379 ARG cc_start: 0.7316 (mtp180) cc_final: 0.7111 (mtp-110) REVERT: B 311 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8046 (pttm) REVERT: B 338 GLU cc_start: 0.8176 (tt0) cc_final: 0.7764 (tt0) REVERT: B 340 LYS cc_start: 0.8510 (mttt) cc_final: 0.8050 (mttm) REVERT: B 369 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7538 (tttt) REVERT: C 311 LYS cc_start: 0.8569 (ttmt) cc_final: 0.7665 (mmtm) REVERT: C 369 LYS cc_start: 0.7630 (ttmt) cc_final: 0.7385 (ttmm) REVERT: C 370 LYS cc_start: 0.8615 (tttt) cc_final: 0.8196 (tttm) REVERT: C 375 LYS cc_start: 0.7604 (ptmt) cc_final: 0.7385 (ptpp) REVERT: D 345 ASP cc_start: 0.7378 (t70) cc_final: 0.6619 (t70) REVERT: D 349 ARG cc_start: 0.7623 (mtm180) cc_final: 0.7367 (mtm180) REVERT: E 311 LYS cc_start: 0.8318 (pttt) cc_final: 0.7963 (ptmt) REVERT: E 340 LYS cc_start: 0.7928 (mttt) cc_final: 0.7554 (mtpm) REVERT: E 345 ASP cc_start: 0.7821 (t0) cc_final: 0.7351 (t0) REVERT: E 349 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6970 (mtp85) REVERT: F 311 LYS cc_start: 0.8176 (pttt) cc_final: 0.7630 (ptmt) REVERT: F 342 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7613 (pm20) REVERT: F 343 LYS cc_start: 0.8072 (ttmt) cc_final: 0.7627 (tttt) outliers start: 5 outliers final: 3 residues processed: 108 average time/residue: 1.3286 time to fit residues: 147.0491 Evaluate side-chains 108 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3429 Z= 0.367 Angle : 0.681 8.020 4590 Z= 0.332 Chirality : 0.051 0.135 519 Planarity : 0.003 0.038 582 Dihedral : 5.002 13.933 450 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.81 % Allowed : 20.16 % Favored : 78.04 % 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: -2.32 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.014 0.002 PHE F 346 TYR 0.026 0.004 TYR D 310 ARG 0.001 0.000 ARG E 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 112 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 0.565 Fit side-chains REVERT: A 338 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6871 (tt0) REVERT: A 340 LYS cc_start: 0.7613 (mttt) cc_final: 0.7231 (mttm) REVERT: A 349 ARG cc_start: 0.7927 (mtt180) cc_final: 0.7665 (mtt-85) REVERT: B 311 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8072 (pttm) REVERT: B 338 GLU cc_start: 0.8174 (tt0) cc_final: 0.7928 (tt0) REVERT: B 340 LYS cc_start: 0.8508 (mttt) cc_final: 0.8179 (mttm) REVERT: B 369 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7597 (tttt) REVERT: C 311 LYS cc_start: 0.8609 (ttmt) cc_final: 0.7727 (mmtm) REVERT: C 369 LYS cc_start: 0.7678 (ttmt) cc_final: 0.7405 (ttmm) REVERT: C 370 LYS cc_start: 0.8621 (tttt) cc_final: 0.8131 (tttm) REVERT: D 349 ARG cc_start: 0.7668 (mtm180) cc_final: 0.7457 (mtm180) REVERT: D 369 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7420 (ttmm) REVERT: E 311 LYS cc_start: 0.8363 (pttt) cc_final: 0.8017 (ptmt) REVERT: E 340 LYS cc_start: 0.7933 (mttt) cc_final: 0.7327 (mttp) REVERT: E 345 ASP cc_start: 0.7819 (t0) cc_final: 0.7352 (t0) REVERT: F 311 LYS cc_start: 0.8192 (pttt) cc_final: 0.7643 (ptmt) REVERT: F 342 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7812 (mp0) REVERT: F 343 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7630 (tttt) REVERT: F 349 ARG cc_start: 0.7735 (mpp80) cc_final: 0.5256 (pmt170) outliers start: 7 outliers final: 4 residues processed: 109 average time/residue: 1.3263 time to fit residues: 148.0414 Evaluate side-chains 107 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.9542 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3429 Z= 0.223 Angle : 0.624 8.156 4590 Z= 0.297 Chirality : 0.049 0.121 519 Planarity : 0.003 0.039 582 Dihedral : 4.720 13.605 450 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.29 % Allowed : 19.90 % 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: -2.29 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.014 0.001 PHE F 346 TYR 0.021 0.002 TYR F 310 ARG 0.001 0.000 ARG E 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 113 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.431 Fit side-chains REVERT: A 338 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6865 (tt0) REVERT: A 340 LYS cc_start: 0.7605 (mttt) cc_final: 0.7210 (mttm) REVERT: A 349 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7681 (mtt-85) REVERT: B 311 LYS cc_start: 0.8686 (ttmt) cc_final: 0.8029 (pttm) REVERT: B 338 GLU cc_start: 0.8177 (tt0) cc_final: 0.7870 (tt0) REVERT: B 340 LYS cc_start: 0.8528 (mttt) cc_final: 0.8206 (mttm) REVERT: B 369 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7587 (tttt) REVERT: C 311 LYS cc_start: 0.8571 (ttmt) cc_final: 0.7689 (mmtm) REVERT: C 369 LYS cc_start: 0.7628 (ttmt) cc_final: 0.7377 (ttmm) REVERT: C 370 LYS cc_start: 0.8621 (tttt) cc_final: 0.8192 (tttm) REVERT: D 345 ASP cc_start: 0.7300 (t70) cc_final: 0.6591 (t70) REVERT: D 349 ARG cc_start: 0.7660 (mtm180) cc_final: 0.7439 (mtm180) REVERT: D 369 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7392 (ttmm) REVERT: E 311 LYS cc_start: 0.8306 (pttt) cc_final: 0.7952 (ptmt) REVERT: E 340 LYS cc_start: 0.7930 (mttt) cc_final: 0.7402 (mttp) REVERT: E 345 ASP cc_start: 0.7801 (t0) cc_final: 0.7354 (t0) REVERT: E 349 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6982 (mtp85) REVERT: E 369 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7632 (ttmm) REVERT: F 311 LYS cc_start: 0.8140 (pttt) cc_final: 0.7577 (ptmt) REVERT: F 342 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7544 (pm20) REVERT: F 343 LYS cc_start: 0.8033 (ttmt) cc_final: 0.7632 (tttt) outliers start: 5 outliers final: 4 residues processed: 111 average time/residue: 1.3806 time to fit residues: 156.8130 Evaluate side-chains 111 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4440 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= 0.267 Angle : 0.651 8.280 4590 Z= 0.313 Chirality : 0.050 0.125 519 Planarity : 0.003 0.019 582 Dihedral : 4.745 13.638 450 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.03 % Allowed : 20.41 % 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: -2.28 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.013 0.001 PHE F 346 TYR 0.027 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 109 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.377 Fit side-chains REVERT: A 338 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6869 (tt0) REVERT: A 340 LYS cc_start: 0.7583 (mttt) cc_final: 0.7209 (mttm) REVERT: A 349 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7660 (mtt-85) REVERT: B 338 GLU cc_start: 0.8177 (tt0) cc_final: 0.7875 (tt0) REVERT: B 340 LYS cc_start: 0.8511 (mttt) cc_final: 0.8184 (mttm) REVERT: B 369 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7572 (tttt) REVERT: C 369 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7397 (ttmm) REVERT: D 349 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7433 (mtm180) REVERT: D 369 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7368 (ttmm) REVERT: E 311 LYS cc_start: 0.8323 (pttt) cc_final: 0.7959 (ptmt) REVERT: E 340 LYS cc_start: 0.7952 (mttt) cc_final: 0.7470 (mttp) REVERT: E 343 LYS cc_start: 0.7885 (ttmt) cc_final: 0.7020 (mmtt) REVERT: E 345 ASP cc_start: 0.7798 (t0) cc_final: 0.7297 (t0) REVERT: E 369 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7625 (ttmm) REVERT: F 311 LYS cc_start: 0.8151 (pttt) cc_final: 0.7602 (ptmt) REVERT: F 342 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7573 (pm20) REVERT: F 343 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7672 (tttt) outliers start: 4 outliers final: 4 residues processed: 108 average time/residue: 1.3419 time to fit residues: 148.3523 Evaluate side-chains 107 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.110723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.099343 restraints weight = 4625.810| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.89 r_work: 0.3376 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3429 Z= 0.194 Angle : 0.618 8.343 4590 Z= 0.293 Chirality : 0.049 0.120 519 Planarity : 0.002 0.017 582 Dihedral : 4.535 13.775 450 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.29 % Allowed : 20.41 % 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: -2.22 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 362 PHE 0.015 0.001 PHE F 346 TYR 0.019 0.002 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: 2688.99 seconds wall clock time: 48 minutes 38.53 seconds (2918.53 seconds total)