Starting phenix.real_space_refine on Sat Dec 9 12:16:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa9_33088/12_2023/7xa9_33088_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa9_33088/12_2023/7xa9_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_33088/12_2023/7xa9_33088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa9_33088/12_2023/7xa9_33088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa9_33088/12_2023/7xa9_33088_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xa9_33088/12_2023/7xa9_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-1.21rc1-5172/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: 6.37, 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: 4.52 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: 2.59 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: 3.37 Time building geometry restraints manager: 4.83 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: 6.610 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: 27.720 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 32.650 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.870 ------------------------------------------------------------------------------- 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 : 1.263 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 198 average time/residue: 1.1112 time to fit residues: 239.9917 Evaluate side-chains 156 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1420 time to fit residues: 2.1207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7985 moved from start: 0.1556 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= 0.262 Angle : 0.610 6.541 15348 Z= 0.321 Chirality : 0.042 0.133 1794 Planarity : 0.006 0.064 1914 Dihedral : 9.039 81.639 1570 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.02 % Allowed : 22.99 % 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: -2.13 (0.19), residues: 1392 helix: -1.31 (0.16), residues: 808 sheet: None (None), residues: 0 loop : -1.38 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 281 HIS 0.003 0.001 HIS A 350 PHE 0.019 0.002 PHE B 317 TYR 0.018 0.002 TYR B 463 ARG 0.002 0.000 ARG B 276 *********************** 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 192 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 1.278 Fit side-chains outliers start: 36 outliers final: 12 residues processed: 178 average time/residue: 0.9920 time to fit residues: 194.7812 Evaluate side-chains 154 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.1742 time to fit residues: 2.8638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 105 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 127 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8012 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11276 Z= 0.279 Angle : 0.579 5.626 15348 Z= 0.299 Chirality : 0.041 0.126 1794 Planarity : 0.005 0.056 1914 Dihedral : 8.350 83.697 1570 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.94 % Allowed : 22.73 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.21), residues: 1392 helix: -0.25 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -0.86 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 87 HIS 0.002 0.001 HIS B 645 PHE 0.017 0.002 PHE B 459 TYR 0.011 0.001 TYR B 463 ARG 0.003 0.000 ARG A 230 *********************** 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 183 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 1.533 Fit side-chains outliers start: 35 outliers final: 18 residues processed: 167 average time/residue: 0.9791 time to fit residues: 181.8935 Evaluate side-chains 144 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 8 average time/residue: 0.5023 time to fit residues: 6.4770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.9990 chunk 95 optimal weight: 0.0770 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 0.0020 overall best weight: 0.5550 ------------------------------------------------------------------------------- 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: 0.8013 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11276 Z= 0.261 Angle : 0.558 5.500 15348 Z= 0.287 Chirality : 0.041 0.122 1794 Planarity : 0.004 0.052 1914 Dihedral : 8.118 84.853 1570 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.69 % Allowed : 21.64 % 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: -0.28 (0.22), residues: 1392 helix: 0.22 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -0.65 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 87 HIS 0.003 0.001 HIS B 327 PHE 0.017 0.002 PHE A 459 TYR 0.011 0.001 TYR B 463 ARG 0.002 0.000 ARG B 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 170 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 1.276 Fit side-chains outliers start: 44 outliers final: 20 residues processed: 158 average time/residue: 0.9152 time to fit residues: 161.2266 Evaluate side-chains 132 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.6904 time to fit residues: 4.8340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2473 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= 0.354 Angle : 0.601 5.388 15348 Z= 0.307 Chirality : 0.043 0.129 1794 Planarity : 0.004 0.049 1914 Dihedral : 8.171 86.407 1570 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.36 % Allowed : 20.47 % Favored : 76.17 % 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: -0.26 (0.22), residues: 1392 helix: 0.25 (0.18), residues: 830 sheet: None (None), residues: 0 loop : -0.67 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 87 HIS 0.003 0.001 HIS A 645 PHE 0.020 0.002 PHE A 417 TYR 0.014 0.002 TYR B 463 ARG 0.003 0.000 ARG B 679 *********************** 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 168 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 1.261 Fit side-chains outliers start: 40 outliers final: 30 residues processed: 156 average time/residue: 0.9706 time to fit residues: 168.0192 Evaluate side-chains 156 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.242 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 8 average time/residue: 0.9643 time to fit residues: 10.3644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11276 Z= 0.315 Angle : 0.577 5.281 15348 Z= 0.296 Chirality : 0.042 0.129 1794 Planarity : 0.004 0.048 1914 Dihedral : 8.070 86.662 1570 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.03 % Allowed : 20.64 % Favored : 75.34 % 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: -0.16 (0.22), residues: 1392 helix: 0.37 (0.17), residues: 838 sheet: None (None), residues: 0 loop : -0.71 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 87 HIS 0.005 0.001 HIS B 327 PHE 0.018 0.002 PHE B 417 TYR 0.016 0.002 TYR B 490 ARG 0.002 0.000 ARG B 679 *********************** 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 184 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 136 time to evaluate : 0.896 Fit side-chains outliers start: 48 outliers final: 26 residues processed: 168 average time/residue: 0.6605 time to fit residues: 123.8974 Evaluate side-chains 150 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 18 residues processed: 8 average time/residue: 0.5581 time to fit residues: 7.7098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.4980 chunk 77 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2574 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= 0.286 Angle : 0.559 5.417 15348 Z= 0.288 Chirality : 0.041 0.125 1794 Planarity : 0.004 0.048 1914 Dihedral : 7.952 86.875 1570 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.10 % Allowed : 21.90 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.22), residues: 1392 helix: 0.48 (0.18), residues: 838 sheet: None (None), residues: 0 loop : -0.69 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.004 0.001 HIS B 327 PHE 0.017 0.002 PHE A 459 TYR 0.018 0.002 TYR B 490 ARG 0.004 0.000 ARG B 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 167 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.148 Fit side-chains outliers start: 37 outliers final: 27 residues processed: 158 average time/residue: 0.9331 time to fit residues: 163.7414 Evaluate side-chains 155 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 22 residues processed: 5 average time/residue: 0.6440 time to fit residues: 5.3750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 0.0570 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 129 optimal weight: 0.3980 overall best weight: 0.2498 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11276 Z= 0.176 Angle : 0.507 5.026 15348 Z= 0.264 Chirality : 0.039 0.121 1794 Planarity : 0.004 0.049 1914 Dihedral : 7.564 88.252 1570 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.19 % Allowed : 22.32 % Favored : 74.50 % 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: 0.44 (0.22), residues: 1392 helix: 0.95 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -0.61 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.003 0.001 HIS A 353 PHE 0.014 0.001 PHE B 459 TYR 0.019 0.001 TYR B 490 ARG 0.004 0.000 ARG B 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 178 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 1.256 Fit side-chains outliers start: 38 outliers final: 24 residues processed: 171 average time/residue: 0.8756 time to fit residues: 167.4046 Evaluate side-chains 152 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 1 average time/residue: 0.2425 time to fit residues: 2.0107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 129 optimal weight: 0.0060 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 chunk 118 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 132 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 327 HIS B 237 ASN B 327 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11276 Z= 0.245 Angle : 0.545 6.508 15348 Z= 0.277 Chirality : 0.041 0.122 1794 Planarity : 0.004 0.048 1914 Dihedral : 7.620 88.379 1570 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.36 % Allowed : 22.82 % Favored : 73.83 % 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: 1.01 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -0.53 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 87 HIS 0.004 0.001 HIS B 327 PHE 0.016 0.002 PHE A 459 TYR 0.019 0.001 TYR B 490 ARG 0.005 0.000 ARG B 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 174 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.200 Fit side-chains outliers start: 40 outliers final: 22 residues processed: 166 average time/residue: 0.9648 time to fit residues: 177.4398 Evaluate side-chains 152 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.7718 time to fit residues: 7.9516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 139 optimal weight: 0.0070 chunk 128 optimal weight: 0.0980 chunk 111 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 overall best weight: 0.3198 ------------------------------------------------------------------------------- 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: 0.7986 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11276 Z= 0.192 Angle : 0.530 6.835 15348 Z= 0.270 Chirality : 0.040 0.137 1794 Planarity : 0.004 0.048 1914 Dihedral : 7.431 89.377 1570 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.18 % Allowed : 23.83 % 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: 0.84 (0.22), residues: 1392 helix: 1.25 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -0.36 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 87 HIS 0.002 0.001 HIS A 208 PHE 0.014 0.001 PHE B 459 TYR 0.021 0.001 TYR A 490 ARG 0.003 0.000 ARG B 233 ********************** 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 160 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.253 Fit side-chains outliers start: 26 outliers final: 20 residues processed: 156 average time/residue: 0.9506 time to fit residues: 165.2070 Evaluate side-chains 152 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 1.5248 time to fit residues: 5.0273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134320 restraints weight = 11631.674| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.24 r_work: 0.3409 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 11276 Z= 0.441 Angle : 0.671 7.591 15348 Z= 0.335 Chirality : 0.046 0.145 1794 Planarity : 0.005 0.049 1914 Dihedral : 8.113 88.209 1570 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.43 % Allowed : 24.08 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.37 (0.22), residues: 1392 helix: 0.80 (0.18), residues: 814 sheet: None (None), residues: 0 loop : -0.44 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 87 HIS 0.005 0.001 HIS B 353 PHE 0.021 0.002 PHE B 417 TYR 0.021 0.002 TYR A 490 ARG 0.003 0.001 ARG B 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3905.40 seconds wall clock time: 73 minutes 26.79 seconds (4406.79 seconds total)