Starting phenix.real_space_refine on Sat Apr 6 01:45:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8u_18261/04_2024/8q8u_18261.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8u_18261/04_2024/8q8u_18261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8u_18261/04_2024/8q8u_18261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8u_18261/04_2024/8q8u_18261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8u_18261/04_2024/8q8u_18261.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8u_18261/04_2024/8q8u_18261.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2046 2.51 5 N 588 2.21 5 O 606 1.98 5 H 3396 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 372": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 372": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 372": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 372": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 372": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 6642 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "B" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "C" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "D" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "E" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "F" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Time building chain proxies: 5.90, per 1000 atoms: 0.89 Number of scatterers: 6642 At special positions: 0 Unit cell: (139.256, 91.464, 33.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 606 8.00 N 588 7.00 C 2046 6.00 H 3396 1.00 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: 5.29 Conformation dependent library (CDL) restraints added in 1.3 seconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 45.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 309 through 310 removed outlier: 6.921A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.794A 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 322 removed outlier: 6.341A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.758A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.939A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 361 removed outlier: 6.764A pdb=" N GLN B 351 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 352 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS B 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY B 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER A 356 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 10.390A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASP C 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ILE C 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 368 through 377 removed outlier: 6.733A pdb=" N ASN A 368 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE C 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N LYS C 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.922A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.795A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 317 through 322 removed outlier: 6.412A pdb=" N LYS D 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N SER E 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR D 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N CYS E 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS D 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL D 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LYS F 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER D 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.510A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 337 through 339 removed outlier: 6.832A pdb=" N GLU D 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.928A pdb=" N ASP D 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 350 through 361 removed outlier: 6.809A pdb=" N GLN E 351 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER D 352 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS E 353 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE D 354 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY E 355 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER D 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N GLN D 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 10.495A pdb=" N ILE F 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N LYS D 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N SER F 356 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY D 355 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASP F 358 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU D 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE F 360 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 368 through 377 removed outlier: 6.772A pdb=" N ASN D 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ILE F 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR F 373 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU D 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N LYS F 375 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS D 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N THR F 377 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU D 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) 49 hydrogen bonds defined for protein. 147 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: 2.00 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.21: 3374 1.21 - 1.48: 1777 1.48 - 1.75: 1535 1.75 - 2.01: 8 2.01 - 2.28: 2 Bond restraints: 6696 Sorted by residual: bond pdb=" N LYS B 343 " pdb=" H BLYS B 343 " ideal model delta sigma weight residual 0.860 2.277 -1.417 2.00e-02 2.50e+03 5.02e+03 bond pdb=" N LYS E 343 " pdb=" H BLYS E 343 " ideal model delta sigma weight residual 0.860 2.243 -1.383 2.00e-02 2.50e+03 4.78e+03 bond pdb=" N LYS A 343 " pdb=" H BLYS A 343 " ideal model delta sigma weight residual 0.860 1.825 -0.965 2.00e-02 2.50e+03 2.33e+03 bond pdb=" N LYS D 343 " pdb=" H BLYS D 343 " ideal model delta sigma weight residual 0.860 1.812 -0.952 2.00e-02 2.50e+03 2.27e+03 bond pdb=" N SER C 341 " pdb=" H BSER C 341 " ideal model delta sigma weight residual 0.860 1.608 -0.748 2.00e-02 2.50e+03 1.40e+03 ... (remaining 6691 not shown) Histogram of bond angle deviations from ideal: 29.36 - 54.15: 10 54.15 - 78.95: 2 78.95 - 103.74: 54 103.74 - 128.54: 12137 128.54 - 153.33: 19 Bond angle restraints: 12222 Sorted by residual: angle pdb=" C GLU C 342 " pdb=" N LYS C 343 " pdb=" H BLYS C 343 " ideal model delta sigma weight residual 124.11 29.36 94.76 3.00e+00 1.11e-01 9.98e+02 angle pdb=" C GLU F 342 " pdb=" N LYS F 343 " pdb=" H BLYS F 343 " ideal model delta sigma weight residual 124.11 30.86 93.26 3.00e+00 1.11e-01 9.66e+02 angle pdb=" C LYS D 340 " pdb=" N SER D 341 " pdb=" H BSER D 341 " ideal model delta sigma weight residual 124.38 35.63 88.75 3.00e+00 1.11e-01 8.75e+02 angle pdb=" C LYS A 340 " pdb=" N SER A 341 " pdb=" H BSER A 341 " ideal model delta sigma weight residual 124.38 36.75 87.63 3.00e+00 1.11e-01 8.53e+02 angle pdb=" C GLU A 342 " pdb=" N LYS A 343 " pdb=" H BLYS A 343 " ideal model delta sigma weight residual 123.95 40.98 82.97 3.00e+00 1.11e-01 7.65e+02 ... (remaining 12217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 2704 17.21 - 34.41: 224 34.41 - 51.61: 79 51.61 - 68.82: 83 68.82 - 86.02: 6 Dihedral angle restraints: 3096 sinusoidal: 1770 harmonic: 1326 Sorted by residual: dihedral pdb=" CA VAL A 350 " pdb=" C VAL A 350 " pdb=" N GLN A 351 " pdb=" CA GLN A 351 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ASN A 368 " pdb=" C ASN A 368 " pdb=" N LYS A 369 " pdb=" CA LYS A 369 " ideal model delta harmonic sigma weight residual 180.00 151.74 28.26 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA VAL F 350 " pdb=" C VAL F 350 " pdb=" N GLN F 351 " pdb=" CA GLN F 351 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 314 0.085 - 0.169: 130 0.169 - 0.254: 37 0.254 - 0.338: 13 0.338 - 0.423: 4 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA LYS A 369 " pdb=" N LYS A 369 " pdb=" C LYS A 369 " pdb=" CB LYS A 369 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA LYS D 369 " pdb=" N LYS D 369 " pdb=" C LYS D 369 " pdb=" CB LYS D 369 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA LYS C 369 " pdb=" N LYS C 369 " pdb=" C LYS C 369 " pdb=" CB LYS C 369 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.85e+00 ... (remaining 495 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 340 " -0.266 2.00e-02 2.50e+03 2.66e-01 7.07e+02 pdb=" N SER D 341 " 0.416 2.00e-02 2.50e+03 pdb=" CA SER D 341 " -0.193 2.00e-02 2.50e+03 pdb=" H BSER D 341 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 340 " -0.256 2.00e-02 2.50e+03 2.65e-01 7.00e+02 pdb=" N SER A 341 " 0.419 2.00e-02 2.50e+03 pdb=" CA SER A 341 " -0.195 2.00e-02 2.50e+03 pdb=" H BSER A 341 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 340 " -0.277 2.00e-02 2.50e+03 2.52e-01 6.34e+02 pdb=" N SER F 341 " 0.371 2.00e-02 2.50e+03 pdb=" CA SER F 341 " -0.179 2.00e-02 2.50e+03 pdb=" H BSER F 341 " 0.085 2.00e-02 2.50e+03 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.63: 25 1.63 - 2.37: 1510 2.37 - 3.12: 20196 3.12 - 3.86: 24486 3.86 - 4.60: 37377 Warning: very small nonbonded interaction distances. Nonbonded interactions: 83594 Sorted by model distance: nonbonded pdb=" HB3 GLU B 342 " pdb=" H BLYS B 343 " model vdw 0.888 2.270 nonbonded pdb=" HB3 GLU E 342 " pdb=" H BLYS E 343 " model vdw 0.977 2.270 nonbonded pdb=" CA GLU C 342 " pdb=" H BLYS C 343 " model vdw 1.089 2.200 nonbonded pdb=" CA GLU F 342 " pdb=" H BLYS F 343 " model vdw 1.125 2.200 nonbonded pdb=" CA GLU A 342 " pdb=" H BLYS A 343 " model vdw 1.169 2.200 ... (remaining 83589 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 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'B' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'C' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'D' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'E' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'F' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.160 Extract box with map and model: 11.500 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.630 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 0.038 3300 Z= 0.750 Angle : 1.968 8.159 4416 Z= 1.301 Chirality : 0.109 0.423 498 Planarity : 0.011 0.049 558 Dihedral : 12.588 86.025 1260 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.81 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.30), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.23), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS C 362 PHE 0.080 0.022 PHE C 346 TYR 0.084 0.029 TYR B 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.5489 time to fit residues: 36.6631 Evaluate side-chains 38 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3300 Z= 0.205 Angle : 0.780 4.666 4416 Z= 0.407 Chirality : 0.052 0.144 498 Planarity : 0.006 0.053 558 Dihedral : 8.291 23.762 432 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % 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: -2.87 (0.31), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.24), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.003 HIS B 330 PHE 0.011 0.002 PHE A 378 TYR 0.012 0.003 TYR B 310 ARG 0.003 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.548 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.3220 time to fit residues: 12.8664 Evaluate side-chains 28 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.0040 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS E 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3300 Z= 0.188 Angle : 0.627 4.054 4416 Z= 0.329 Chirality : 0.050 0.143 498 Planarity : 0.006 0.048 558 Dihedral : 6.736 18.818 432 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.08 % Allowed : 8.60 % Favored : 90.32 % 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: -2.81 (0.32), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 330 PHE 0.012 0.002 PHE D 346 TYR 0.014 0.003 TYR F 310 ARG 0.005 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.561 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.3575 time to fit residues: 12.9011 Evaluate side-chains 28 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain E residue 351 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3300 Z= 0.294 Angle : 0.650 4.749 4416 Z= 0.345 Chirality : 0.051 0.143 498 Planarity : 0.006 0.049 558 Dihedral : 6.382 17.518 432 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.08 % Allowed : 9.41 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.33), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS F 362 PHE 0.017 0.002 PHE D 346 TYR 0.017 0.003 TYR F 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.3923 time to fit residues: 13.5676 Evaluate side-chains 28 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3300 Z= 0.157 Angle : 0.548 3.946 4416 Z= 0.286 Chirality : 0.049 0.133 498 Planarity : 0.005 0.044 558 Dihedral : 5.742 15.839 432 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.54 % Allowed : 9.41 % Favored : 90.05 % 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: -2.75 (0.34), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 330 PHE 0.007 0.001 PHE C 346 TYR 0.011 0.003 TYR D 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.2586 time to fit residues: 10.9971 Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain E residue 351 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3300 Z= 0.193 Angle : 0.544 3.920 4416 Z= 0.285 Chirality : 0.049 0.132 498 Planarity : 0.005 0.044 558 Dihedral : 5.571 15.554 432 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.54 % Allowed : 9.41 % Favored : 90.05 % 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: -2.74 (0.34), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 362 PHE 0.010 0.001 PHE A 346 TYR 0.010 0.003 TYR F 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.751 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.2696 time to fit residues: 11.0484 Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain E residue 351 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.0270 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS F 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3300 Z= 0.140 Angle : 0.509 3.731 4416 Z= 0.260 Chirality : 0.048 0.131 498 Planarity : 0.005 0.040 558 Dihedral : 5.138 14.587 432 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.54 % Allowed : 9.68 % Favored : 89.78 % 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: -2.50 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 330 PHE 0.011 0.001 PHE A 378 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 31 average time/residue: 0.2591 time to fit residues: 10.7090 Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain E residue 351 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3300 Z= 0.144 Angle : 0.499 3.778 4416 Z= 0.254 Chirality : 0.048 0.129 498 Planarity : 0.005 0.038 558 Dihedral : 5.005 14.361 432 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.54 % Allowed : 9.95 % Favored : 89.52 % 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 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 362 PHE 0.006 0.001 PHE A 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.2711 time to fit residues: 10.8763 Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain E residue 351 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3300 Z= 0.189 Angle : 0.511 3.892 4416 Z= 0.264 Chirality : 0.048 0.130 498 Planarity : 0.005 0.039 558 Dihedral : 5.017 14.310 432 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.54 % Allowed : 9.95 % Favored : 89.52 % 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 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 362 PHE 0.009 0.002 PHE A 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.570 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.2634 time to fit residues: 10.3941 Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain E residue 351 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.0470 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3300 Z= 0.157 Angle : 0.501 3.892 4416 Z= 0.256 Chirality : 0.048 0.128 498 Planarity : 0.005 0.040 558 Dihedral : 4.926 13.507 432 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.54 % Allowed : 9.95 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 362 PHE 0.007 0.001 PHE B 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG F 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.571 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.2773 time to fit residues: 11.2000 Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain E residue 351 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** 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 = 0.5641 r_free = 0.5641 target = 0.396510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.6275 r_free = 0.6275 target = 0.336341 restraints weight = 29775.957| |-----------------------------------------------------------------------------| r_work (start): 0.5569 rms_B_bonded: 1.49 r_work: 0.6258 rms_B_bonded: 0.59 restraints_weight: 0.5000 r_work: 0.6208 rms_B_bonded: 0.77 restraints_weight: 0.2500 r_work: 0.6063 rms_B_bonded: 3.06 restraints_weight: 0.1250 r_work (final): 0.6063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5527 r_free = 0.5527 target_work(ls_wunit_k1) = 0.382 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5527 r_free = 0.5527 target_work(ls_wunit_k1) = 0.382 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.5527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3300 Z= 0.174 Angle : 0.503 3.882 4416 Z= 0.257 Chirality : 0.048 0.131 498 Planarity : 0.005 0.040 558 Dihedral : 4.859 12.998 432 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.54 % Allowed : 10.48 % Favored : 88.98 % 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: -2.14 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 362 PHE 0.010 0.002 PHE E 378 TYR 0.009 0.002 TYR A 310 ARG 0.001 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2579.93 seconds wall clock time: 46 minutes 19.22 seconds (2779.22 seconds total)