Starting phenix.real_space_refine on Thu Feb 15 03:52:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa9_33088/02_2024/7xa9_33088_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa9_33088/02_2024/7xa9_33088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa9_33088/02_2024/7xa9_33088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa9_33088/02_2024/7xa9_33088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa9_33088/02_2024/7xa9_33088_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa9_33088/02_2024/7xa9_33088_updated.pdb" } resolution = 2.84 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= 0.026 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 7140 2.51 5 N 1844 2.21 5 O 1978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ARG 295": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "A ARG 755": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ARG 295": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 523": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B GLU 591": "OE1" <-> "OE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B ARG 616": "NH1" <-> "NH2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B GLU 666": "OE1" <-> "OE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 678": "OE1" <-> "OE2" Residue "B ARG 724": "NH1" <-> "NH2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "B ARG 755": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11028 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5470 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 29, 'TRANS': 672} Chain breaks: 2 Chain: "B" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5470 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 29, 'TRANS': 672} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' MG': 1, 'ATP': 1, 'NO3': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' MG': 1, 'ATP': 1, 'NO3': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.35, per 1000 atoms: 0.58 Number of scatterers: 11028 At special positions: 0 Unit cell: (77.9, 104.14, 104.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 2 11.99 O 1978 8.00 N 1844 7.00 C 7140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 306 " distance=2.35 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 419 " distance=2.36 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 405 " distance=2.29 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 306 " distance=2.35 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 419 " distance=2.36 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 405 " distance=2.29 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: 4.23 Conformation dependent library (CDL) restraints added in 2.2 seconds 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 6 sheets defined 54.1% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 76 through 124 removed outlier: 3.586A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 153 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 180 through 195 removed outlier: 3.745A pdb=" N ALA A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.611A pdb=" N VAL A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 4.437A pdb=" N TYR A 234 " --> pdb=" O TRP A 231 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 257 removed outlier: 3.721A pdb=" N ASP A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 277 through 299 removed outlier: 3.915A pdb=" N ARG A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 332 through 363 removed outlier: 3.603A pdb=" N ILE A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 386 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 480 through 497 Processing helix chain 'A' and resid 506 through 522 removed outlier: 3.642A pdb=" N VAL A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 536 Processing helix chain 'A' and resid 542 through 558 removed outlier: 3.681A pdb=" N SER A 558 " --> pdb=" O THR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 570 removed outlier: 3.571A pdb=" N ILE A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 608 through 616 Processing helix chain 'A' and resid 643 through 651 Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.560A pdb=" N ALA A 677 " --> pdb=" O PRO A 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 677' Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 716 through 725 Processing helix chain 'A' and resid 751 through 754 No H-bonds generated for 'chain 'A' and resid 751 through 754' Processing helix chain 'A' and resid 756 through 762 removed outlier: 3.546A pdb=" N ALA A 762 " --> pdb=" O ASN A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 76 through 124 removed outlier: 3.586A pdb=" N PHE B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 153 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.745A pdb=" N ALA B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 219 removed outlier: 3.611A pdb=" N VAL B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 4.437A pdb=" N TYR B 234 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 257 removed outlier: 3.721A pdb=" N ASP B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 277 through 299 removed outlier: 3.915A pdb=" N ARG B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 332 through 363 removed outlier: 3.603A pdb=" N ILE B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 386 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 437 through 442 Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 480 through 497 Processing helix chain 'B' and resid 506 through 522 removed outlier: 3.642A pdb=" N VAL B 511 " --> pdb=" O GLY B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 536 Processing helix chain 'B' and resid 542 through 558 removed outlier: 3.681A pdb=" N SER B 558 " --> pdb=" O THR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 570 removed outlier: 3.571A pdb=" N ILE B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 594 Processing helix chain 'B' and resid 608 through 616 Processing helix chain 'B' and resid 643 through 651 Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.560A pdb=" N ALA B 677 " --> pdb=" O PRO B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 677' Processing helix chain 'B' and resid 692 through 694 No H-bonds generated for 'chain 'B' and resid 692 through 694' Processing helix chain 'B' and resid 716 through 725 Processing helix chain 'B' and resid 751 through 754 No H-bonds generated for 'chain 'B' and resid 751 through 754' Processing helix chain 'B' and resid 756 through 762 removed outlier: 3.546A pdb=" N ALA B 762 " --> pdb=" O ASN B 758 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 605 through 607 Processing sheet with id= B, first strand: chain 'A' and resid 622 through 625 removed outlier: 3.590A pdb=" N GLY A 639 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 709 through 711 removed outlier: 6.282A pdb=" N LEU A 732 " --> pdb=" O VAL A 710 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 605 through 607 Processing sheet with id= E, first strand: chain 'B' and resid 622 through 625 removed outlier: 3.590A pdb=" N GLY B 639 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 709 through 711 removed outlier: 6.282A pdb=" N LEU B 732 " --> pdb=" O VAL B 710 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1554 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: 3.73 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1794 1.32 - 1.44: 3034 1.44 - 1.56: 6346 1.56 - 1.69: 12 1.69 - 1.81: 90 Bond restraints: 11276 Sorted by residual: bond pdb=" C GLN A 416 " pdb=" N PHE A 417 " ideal model delta sigma weight residual 1.334 1.440 -0.106 1.41e-02 5.03e+03 5.69e+01 bond pdb=" C GLN B 416 " pdb=" N PHE B 417 " ideal model delta sigma weight residual 1.334 1.440 -0.106 1.41e-02 5.03e+03 5.69e+01 bond pdb=" C5 ATP B 904 " pdb=" C6 ATP B 904 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.69e+01 bond pdb=" C5 ATP A 904 " pdb=" C6 ATP A 904 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.69e+01 bond pdb=" C4 ATP B 904 " pdb=" C5 ATP B 904 " ideal model delta sigma weight residual 1.388 1.452 -0.064 1.00e-02 1.00e+04 4.14e+01 ... (remaining 11271 not shown) Histogram of bond angle deviations from ideal: 95.89 - 104.38: 202 104.38 - 112.87: 5858 112.87 - 121.37: 6458 121.37 - 129.86: 2730 129.86 - 138.35: 100 Bond angle restraints: 15348 Sorted by residual: angle pdb=" PA ATP A 904 " pdb=" O3A ATP A 904 " pdb=" PB ATP A 904 " ideal model delta sigma weight residual 136.83 120.86 15.97 1.00e+00 1.00e+00 2.55e+02 angle pdb=" PA ATP B 904 " pdb=" O3A ATP B 904 " pdb=" PB ATP B 904 " ideal model delta sigma weight residual 136.83 120.86 15.97 1.00e+00 1.00e+00 2.55e+02 angle pdb=" PB ATP B 904 " pdb=" O3B ATP B 904 " pdb=" PG ATP B 904 " ideal model delta sigma weight residual 139.87 125.63 14.24 1.00e+00 1.00e+00 2.03e+02 angle pdb=" PB ATP A 904 " pdb=" O3B ATP A 904 " pdb=" PG ATP A 904 " ideal model delta sigma weight residual 139.87 125.63 14.24 1.00e+00 1.00e+00 2.03e+02 angle pdb=" N LYS A 202 " pdb=" CA LYS A 202 " pdb=" C LYS A 202 " ideal model delta sigma weight residual 112.59 102.56 10.03 1.22e+00 6.72e-01 6.76e+01 ... (remaining 15343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5730 17.71 - 35.43: 728 35.43 - 53.14: 130 53.14 - 70.85: 32 70.85 - 88.57: 18 Dihedral angle restraints: 6638 sinusoidal: 2622 harmonic: 4016 Sorted by residual: dihedral pdb=" CB CYS A 301 " pdb=" SG CYS A 301 " pdb=" SG CYS A 306 " pdb=" CB CYS A 306 " ideal model delta sinusoidal sigma weight residual -86.00 -30.10 -55.90 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS B 301 " pdb=" SG CYS B 301 " pdb=" SG CYS B 306 " pdb=" CB CYS B 306 " ideal model delta sinusoidal sigma weight residual -86.00 -30.10 -55.90 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CA GLU A 270 " pdb=" C GLU A 270 " pdb=" N VAL A 271 " pdb=" CA VAL A 271 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 6635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1022 0.047 - 0.095: 524 0.095 - 0.142: 164 0.142 - 0.190: 62 0.190 - 0.237: 22 Chirality restraints: 1794 Sorted by residual: chirality pdb=" CA LYS B 202 " pdb=" N LYS B 202 " pdb=" C LYS B 202 " pdb=" CB LYS B 202 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LYS A 202 " pdb=" N LYS A 202 " pdb=" C LYS A 202 " pdb=" CB LYS A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL A 291 " pdb=" CA VAL A 291 " pdb=" CG1 VAL A 291 " pdb=" CG2 VAL A 291 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1791 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 278 " -0.025 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C ALA B 278 " 0.084 2.00e-02 2.50e+03 pdb=" O ALA B 278 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU B 279 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 278 " -0.025 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C ALA A 278 " 0.084 2.00e-02 2.50e+03 pdb=" O ALA A 278 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU A 279 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 289 " -0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C VAL A 289 " 0.075 2.00e-02 2.50e+03 pdb=" O VAL A 289 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL A 290 " -0.026 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 94 2.53 - 3.12: 6850 3.12 - 3.72: 18608 3.72 - 4.31: 27661 4.31 - 4.90: 44665 Nonbonded interactions: 97878 Sorted by model distance: nonbonded pdb=" OE1 GLU A 55 " pdb="MG MG A 905 " model vdw 1.938 2.170 nonbonded pdb=" OE1 GLU B 55 " pdb="MG MG B 905 " model vdw 1.938 2.170 nonbonded pdb=" O2B ATP A 904 " pdb="MG MG A 905 " model vdw 2.121 2.170 nonbonded pdb=" O2B ATP B 904 " pdb="MG MG B 905 " model vdw 2.121 2.170 nonbonded pdb=" OD2 ASP A 753 " pdb=" O2' ATP A 904 " model vdw 2.327 2.440 ... (remaining 97873 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' selection = chain 'B' } 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: 10.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 28.250 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 34.020 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 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:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.010 0.106 11276 Z= 0.675 Angle : 1.334 15.970 15348 Z= 0.794 Chirality : 0.067 0.237 1794 Planarity : 0.011 0.094 1914 Dihedral : 16.618 88.565 4044 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.17 % Allowed : 22.15 % Favored : 77.68 % 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: -5.02 (0.15), residues: 1392 helix: -3.91 (0.09), residues: 820 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 274 HIS 0.013 0.002 HIS A 208 PHE 0.035 0.004 PHE A 317 TYR 0.031 0.003 TYR A 490 ARG 0.003 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 1.323 Fit side-chains REVERT: A 122 TYR cc_start: 0.7860 (m-80) cc_final: 0.7429 (m-80) REVERT: A 243 ASP cc_start: 0.8021 (m-30) cc_final: 0.7821 (m-30) REVERT: A 268 LEU cc_start: 0.8651 (tt) cc_final: 0.8417 (tp) REVERT: A 276 ARG cc_start: 0.8301 (mtm180) cc_final: 0.8075 (mtm180) REVERT: A 449 ASN cc_start: 0.7717 (m-40) cc_final: 0.7414 (m-40) REVERT: B 122 TYR cc_start: 0.7860 (m-80) cc_final: 0.7429 (m-80) REVERT: B 268 LEU cc_start: 0.8650 (tt) cc_final: 0.8417 (tp) REVERT: B 276 ARG cc_start: 0.8296 (mtm180) cc_final: 0.8070 (mtm180) REVERT: B 449 ASN cc_start: 0.7715 (m-40) cc_final: 0.7413 (m-40) outliers start: 2 outliers final: 2 residues processed: 198 average time/residue: 1.1184 time to fit residues: 240.5411 Evaluate side-chains 158 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain B residue 483 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 537 ASN B 170 ASN B 537 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11276 Z= 0.265 Angle : 0.610 6.346 15348 Z= 0.321 Chirality : 0.042 0.133 1794 Planarity : 0.006 0.065 1914 Dihedral : 9.109 82.710 1574 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.52 % Allowed : 23.41 % Favored : 74.08 % 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 (0.19), residues: 1392 helix: -1.33 (0.16), residues: 810 sheet: None (None), residues: 0 loop : -1.36 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 87 HIS 0.003 0.001 HIS A 350 PHE 0.018 0.002 PHE B 317 TYR 0.018 0.002 TYR B 463 ARG 0.002 0.000 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 1.268 Fit side-chains REVERT: A 122 TYR cc_start: 0.7779 (m-80) cc_final: 0.7430 (m-80) REVERT: A 233 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6416 (ptp-170) REVERT: A 276 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7902 (mtm180) REVERT: A 365 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7799 (mtmt) REVERT: A 449 ASN cc_start: 0.7788 (m-40) cc_final: 0.7586 (m110) REVERT: A 636 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7003 (tt0) REVERT: A 693 MET cc_start: 0.8550 (mmm) cc_final: 0.8236 (tpt) REVERT: B 122 TYR cc_start: 0.7781 (m-80) cc_final: 0.7430 (m-80) REVERT: B 233 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6416 (ptp-170) REVERT: B 365 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7799 (mtmt) REVERT: B 449 ASN cc_start: 0.7789 (m-40) cc_final: 0.7585 (m110) REVERT: B 636 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7003 (tt0) REVERT: B 693 MET cc_start: 0.8552 (mmm) cc_final: 0.8238 (tpt) outliers start: 30 outliers final: 12 residues processed: 177 average time/residue: 1.0007 time to fit residues: 195.0082 Evaluate side-chains 153 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 126 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11276 Z= 0.263 Angle : 0.566 5.616 15348 Z= 0.294 Chirality : 0.040 0.127 1794 Planarity : 0.005 0.057 1914 Dihedral : 8.271 83.914 1570 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.85 % Allowed : 23.15 % Favored : 73.99 % 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: -0.88 (0.21), residues: 1392 helix: -0.25 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -0.94 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 87 HIS 0.002 0.001 HIS A 645 PHE 0.017 0.002 PHE A 459 TYR 0.010 0.001 TYR A 463 ARG 0.003 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.269 Fit side-chains REVERT: A 122 TYR cc_start: 0.7775 (m-80) cc_final: 0.7465 (m-80) REVERT: A 233 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6608 (ptp-170) REVERT: A 276 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7908 (mtm180) REVERT: A 365 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7747 (mtmt) REVERT: A 393 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7007 (pm20) REVERT: A 449 ASN cc_start: 0.7844 (m-40) cc_final: 0.7582 (m110) REVERT: A 483 ILE cc_start: 0.8390 (mt) cc_final: 0.8179 (mt) REVERT: B 122 TYR cc_start: 0.7778 (m-80) cc_final: 0.7464 (m-80) REVERT: B 233 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.6607 (ptp-170) REVERT: B 276 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7970 (mtm180) REVERT: B 365 LYS cc_start: 0.7997 (mtpp) cc_final: 0.7748 (mtmt) REVERT: B 393 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7007 (pm20) REVERT: B 449 ASN cc_start: 0.7840 (m-40) cc_final: 0.7581 (m110) REVERT: B 483 ILE cc_start: 0.8389 (mt) cc_final: 0.8181 (mt) outliers start: 34 outliers final: 14 residues processed: 169 average time/residue: 1.0722 time to fit residues: 198.6932 Evaluate side-chains 157 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 672 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 66 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 538 ASN B 327 HIS B 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11276 Z= 0.276 Angle : 0.559 5.490 15348 Z= 0.288 Chirality : 0.041 0.123 1794 Planarity : 0.004 0.052 1914 Dihedral : 8.112 85.397 1570 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.53 % Allowed : 20.81 % Favored : 74.66 % 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: -0.52 (0.21), residues: 1392 helix: 0.11 (0.17), residues: 840 sheet: None (None), residues: 0 loop : -0.92 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 87 HIS 0.002 0.001 HIS B 645 PHE 0.017 0.002 PHE B 459 TYR 0.011 0.002 TYR A 463 ARG 0.003 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 134 time to evaluate : 1.367 Fit side-chains REVERT: A 85 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8285 (mp) REVERT: A 122 TYR cc_start: 0.7771 (m-80) cc_final: 0.7492 (m-80) REVERT: A 233 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.6713 (ptp-170) REVERT: A 276 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7834 (mtm180) REVERT: A 365 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7737 (mtmt) REVERT: A 393 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6958 (pm20) REVERT: A 449 ASN cc_start: 0.7838 (m-40) cc_final: 0.7622 (m110) REVERT: A 483 ILE cc_start: 0.8377 (mt) cc_final: 0.8170 (mt) REVERT: A 581 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: A 636 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6899 (tt0) REVERT: B 85 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8292 (mp) REVERT: B 122 TYR cc_start: 0.7772 (m-80) cc_final: 0.7493 (m-80) REVERT: B 233 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6715 (ptp-170) REVERT: B 365 LYS cc_start: 0.7981 (mtpp) cc_final: 0.7739 (mtmt) REVERT: B 393 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6957 (pm20) REVERT: B 449 ASN cc_start: 0.7836 (m-40) cc_final: 0.7623 (m110) REVERT: B 483 ILE cc_start: 0.8376 (mt) cc_final: 0.8168 (mt) REVERT: B 636 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6896 (tt0) outliers start: 54 outliers final: 20 residues processed: 172 average time/residue: 1.0042 time to fit residues: 190.7022 Evaluate side-chains 150 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 121 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 538 ASN B 327 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11276 Z= 0.238 Angle : 0.533 5.205 15348 Z= 0.275 Chirality : 0.040 0.120 1794 Planarity : 0.004 0.051 1914 Dihedral : 7.892 86.534 1570 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.69 % Allowed : 21.22 % Favored : 75.08 % 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: -0.12 (0.22), residues: 1392 helix: 0.42 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.75 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS B 350 PHE 0.016 0.002 PHE B 459 TYR 0.010 0.001 TYR A 490 ARG 0.003 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 1.398 Fit side-chains REVERT: A 85 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8265 (mp) REVERT: A 122 TYR cc_start: 0.7743 (m-80) cc_final: 0.7490 (m-80) REVERT: A 233 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.6733 (ptp-170) REVERT: A 276 ARG cc_start: 0.8073 (mtm180) cc_final: 0.7758 (mtm180) REVERT: A 393 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: A 449 ASN cc_start: 0.7862 (m-40) cc_final: 0.7654 (m110) REVERT: A 636 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6872 (tt0) REVERT: B 85 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8266 (mp) REVERT: B 122 TYR cc_start: 0.7745 (m-80) cc_final: 0.7492 (m-80) REVERT: B 233 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.6735 (ptp-170) REVERT: B 268 LEU cc_start: 0.8617 (tt) cc_final: 0.8411 (tp) REVERT: B 393 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: B 449 ASN cc_start: 0.7857 (m-40) cc_final: 0.7652 (m110) REVERT: B 636 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6870 (tt0) outliers start: 44 outliers final: 18 residues processed: 164 average time/residue: 0.9871 time to fit residues: 178.5676 Evaluate side-chains 160 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 112 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11276 Z= 0.284 Angle : 0.558 5.309 15348 Z= 0.286 Chirality : 0.042 0.126 1794 Planarity : 0.004 0.049 1914 Dihedral : 7.884 87.193 1570 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.11 % Allowed : 20.72 % Favored : 75.17 % 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: -0.00 (0.22), residues: 1392 helix: 0.51 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.68 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 87 HIS 0.003 0.001 HIS A 645 PHE 0.016 0.002 PHE A 459 TYR 0.014 0.002 TYR A 490 ARG 0.003 0.000 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 138 time to evaluate : 1.204 Fit side-chains REVERT: A 85 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 103 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7694 (tp) REVERT: A 122 TYR cc_start: 0.7745 (m-80) cc_final: 0.7506 (m-80) REVERT: A 233 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.6787 (ptp-170) REVERT: A 276 ARG cc_start: 0.8150 (mtm180) cc_final: 0.7917 (mtm180) REVERT: A 393 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6859 (pm20) REVERT: A 449 ASN cc_start: 0.7872 (m-40) cc_final: 0.7669 (m110) REVERT: A 636 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6883 (tt0) REVERT: B 85 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8266 (mp) REVERT: B 103 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7698 (tp) REVERT: B 122 TYR cc_start: 0.7747 (m-80) cc_final: 0.7506 (m-80) REVERT: B 233 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.6774 (ptp-170) REVERT: B 393 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: B 636 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6879 (tt0) outliers start: 49 outliers final: 25 residues processed: 167 average time/residue: 0.8897 time to fit residues: 165.9938 Evaluate side-chains 170 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 135 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11276 Z= 0.298 Angle : 0.568 5.661 15348 Z= 0.290 Chirality : 0.042 0.131 1794 Planarity : 0.004 0.049 1914 Dihedral : 7.884 87.391 1570 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.94 % Allowed : 21.81 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.22), residues: 1392 helix: 0.55 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.64 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 87 HIS 0.002 0.001 HIS B 645 PHE 0.017 0.002 PHE A 459 TYR 0.018 0.002 TYR B 490 ARG 0.003 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 139 time to evaluate : 1.319 Fit side-chains REVERT: A 85 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8290 (mp) REVERT: A 103 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7706 (tp) REVERT: A 122 TYR cc_start: 0.7757 (m-80) cc_final: 0.7524 (m-80) REVERT: A 233 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6782 (ptp-170) REVERT: A 276 ARG cc_start: 0.8192 (mtm180) cc_final: 0.7811 (mtm180) REVERT: A 393 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6918 (pm20) REVERT: A 636 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6858 (tt0) REVERT: B 85 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8323 (mp) REVERT: B 103 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7710 (tp) REVERT: B 122 TYR cc_start: 0.7758 (m-80) cc_final: 0.7523 (m-80) REVERT: B 233 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.6775 (ptp-170) REVERT: B 393 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6921 (pm20) REVERT: B 636 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6853 (tt0) outliers start: 47 outliers final: 25 residues processed: 167 average time/residue: 0.9413 time to fit residues: 174.9639 Evaluate side-chains 167 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 0.0980 chunk 91 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 129 optimal weight: 0.0970 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 694 GLN B 694 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11276 Z= 0.191 Angle : 0.511 5.049 15348 Z= 0.264 Chirality : 0.039 0.122 1794 Planarity : 0.004 0.049 1914 Dihedral : 7.528 88.557 1570 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.10 % Allowed : 22.65 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.35 (0.22), residues: 1392 helix: 0.80 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.56 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 87 HIS 0.002 0.000 HIS A 208 PHE 0.014 0.001 PHE A 459 TYR 0.019 0.001 TYR A 490 ARG 0.003 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 149 time to evaluate : 1.251 Fit side-chains REVERT: A 85 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8207 (mp) REVERT: A 122 TYR cc_start: 0.7738 (m-80) cc_final: 0.7475 (m-80) REVERT: A 233 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.6706 (ptp-170) REVERT: A 276 ARG cc_start: 0.8075 (mtm180) cc_final: 0.7863 (mtm180) REVERT: A 393 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6879 (pm20) REVERT: A 636 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6876 (tt0) REVERT: B 85 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8220 (mp) REVERT: B 122 TYR cc_start: 0.7740 (m-80) cc_final: 0.7474 (m-80) REVERT: B 233 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6626 (ptp-170) REVERT: B 393 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6879 (pm20) REVERT: B 636 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6873 (tt0) outliers start: 37 outliers final: 18 residues processed: 171 average time/residue: 0.9729 time to fit residues: 183.9050 Evaluate side-chains 156 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 chunk 118 optimal weight: 0.5980 chunk 82 optimal weight: 0.0470 chunk 132 optimal weight: 0.7980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 694 GLN B 694 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11276 Z= 0.196 Angle : 0.513 5.151 15348 Z= 0.264 Chirality : 0.040 0.122 1794 Planarity : 0.004 0.049 1914 Dihedral : 7.412 88.982 1570 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.36 % Allowed : 22.99 % Favored : 73.66 % 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: 0.53 (0.22), residues: 1392 helix: 0.94 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.47 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 583 HIS 0.002 0.001 HIS B 208 PHE 0.014 0.001 PHE A 459 TYR 0.020 0.001 TYR B 490 ARG 0.003 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 1.356 Fit side-chains REVERT: A 85 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8196 (mp) REVERT: A 103 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7714 (tp) REVERT: A 109 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: A 122 TYR cc_start: 0.7724 (m-80) cc_final: 0.7463 (m-80) REVERT: A 233 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.6690 (ptp-170) REVERT: A 393 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: A 636 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: B 85 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8253 (mp) REVERT: B 86 LYS cc_start: 0.7792 (ptpp) cc_final: 0.7067 (mmtp) REVERT: B 103 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7701 (tp) REVERT: B 109 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: B 122 TYR cc_start: 0.7724 (m-80) cc_final: 0.7461 (m-80) REVERT: B 393 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6858 (pm20) REVERT: B 636 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6882 (tt0) outliers start: 40 outliers final: 18 residues processed: 174 average time/residue: 0.9470 time to fit residues: 182.8087 Evaluate side-chains 163 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11276 Z= 0.321 Angle : 0.594 6.176 15348 Z= 0.300 Chirality : 0.043 0.128 1794 Planarity : 0.004 0.049 1914 Dihedral : 7.819 87.909 1570 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.02 % Allowed : 23.32 % Favored : 73.66 % 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: 0.36 (0.22), residues: 1392 helix: 0.78 (0.18), residues: 838 sheet: None (None), residues: 0 loop : -0.49 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 87 HIS 0.003 0.001 HIS A 645 PHE 0.017 0.002 PHE A 459 TYR 0.022 0.002 TYR B 490 ARG 0.008 0.000 ARG B 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.261 Fit side-chains REVERT: A 103 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7706 (tp) REVERT: A 109 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6682 (mt-10) REVERT: A 122 TYR cc_start: 0.7741 (m-80) cc_final: 0.7535 (m-80) REVERT: A 233 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6747 (ptp-170) REVERT: A 393 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6869 (pm20) REVERT: B 85 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8286 (mp) REVERT: B 103 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7695 (tp) REVERT: B 109 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6682 (mt-10) REVERT: B 122 TYR cc_start: 0.7742 (m-80) cc_final: 0.7535 (m-80) REVERT: B 393 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6869 (pm20) outliers start: 36 outliers final: 16 residues processed: 165 average time/residue: 1.0244 time to fit residues: 186.8021 Evaluate side-chains 164 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 16 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 0.0980 chunk 46 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS B 327 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.155201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.139752 restraints weight = 11613.631| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.24 r_work: 0.3479 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11276 Z= 0.220 Angle : 0.539 5.325 15348 Z= 0.276 Chirality : 0.040 0.124 1794 Planarity : 0.004 0.049 1914 Dihedral : 7.577 88.683 1570 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.27 % Allowed : 24.50 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.22), residues: 1392 helix: 0.93 (0.18), residues: 838 sheet: None (None), residues: 0 loop : -0.39 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 87 HIS 0.003 0.001 HIS B 327 PHE 0.015 0.001 PHE B 459 TYR 0.022 0.001 TYR B 490 ARG 0.004 0.000 ARG B 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4118.61 seconds wall clock time: 74 minutes 19.19 seconds (4459.19 seconds total)