Starting phenix.real_space_refine on Sun Feb 18 10:01:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fw9_29498/02_2024/8fw9_29498_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fw9_29498/02_2024/8fw9_29498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fw9_29498/02_2024/8fw9_29498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fw9_29498/02_2024/8fw9_29498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fw9_29498/02_2024/8fw9_29498_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fw9_29498/02_2024/8fw9_29498_neut.pdb" } resolution = 4.46 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 13824 2.51 5 N 3660 2.21 5 O 4017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 980": "OD1" <-> "OD2" Residue "A PHE 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 576": "OE1" <-> "OE2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21612 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Chain: "B" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Chain: "C" Number of atoms: 7204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7204 Classifications: {'peptide': 904} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 878} Chain breaks: 1 Time building chain proxies: 11.37, per 1000 atoms: 0.53 Number of scatterers: 21612 At special positions: 0 Unit cell: (163.056, 199.08, 95.748, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4017 8.00 N 3660 7.00 C 13824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.31 Conformation dependent library (CDL) restraints added in 4.0 seconds 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5130 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 20 sheets defined 48.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 94 through 109 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 230 through 240 removed outlier: 4.070A pdb=" N ALA A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 314 through 328 Processing helix chain 'A' and resid 329 through 335 removed outlier: 4.010A pdb=" N ASN A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.729A pdb=" N ASN A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 418 through 425 Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 463 through 475 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 487 through 498 removed outlier: 3.574A pdb=" N SER A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 Processing helix chain 'A' and resid 541 through 565 Processing helix chain 'A' and resid 573 through 580 removed outlier: 3.806A pdb=" N ALA A 577 " --> pdb=" O GLN A 573 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 602 removed outlier: 3.546A pdb=" N ASP A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.598A pdb=" N VAL A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 686 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 779 through 789 removed outlier: 3.994A pdb=" N ASN A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 863 through 873 removed outlier: 3.516A pdb=" N ALA A 867 " --> pdb=" O ASP A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 894 Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.803A pdb=" N LEU A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 901 " --> pdb=" O SER A 897 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N HIS A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 931 Processing helix chain 'A' and resid 954 through 958 Processing helix chain 'A' and resid 980 through 993 Processing helix chain 'A' and resid 1008 through 1015 Processing helix chain 'B' and resid 95 through 109 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 231 through 240 removed outlier: 4.359A pdb=" N ARG B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 258 through 267 Processing helix chain 'B' and resid 268 through 271 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 342 through 347 removed outlier: 3.547A pdb=" N ALA B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 Processing helix chain 'B' and resid 375 through 378 Processing helix chain 'B' and resid 382 through 403 Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'B' and resid 418 through 425 Processing helix chain 'B' and resid 443 through 460 Processing helix chain 'B' and resid 463 through 475 Processing helix chain 'B' and resid 479 through 484 Processing helix chain 'B' and resid 487 through 498 removed outlier: 3.608A pdb=" N SER B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 512 Processing helix chain 'B' and resid 541 through 564 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.713A pdb=" N PHE B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 602 removed outlier: 3.999A pdb=" N ASP B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 609 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.537A pdb=" N VAL B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 686 Processing helix chain 'B' and resid 703 through 709 Processing helix chain 'B' and resid 725 through 735 Processing helix chain 'B' and resid 778 through 788 Processing helix chain 'B' and resid 807 through 815 Processing helix chain 'B' and resid 833 through 844 Processing helix chain 'B' and resid 863 through 873 Processing helix chain 'B' and resid 891 through 894 Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.623A pdb=" N LEU B 900 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS B 901 " --> pdb=" O SER B 897 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N HIS B 902 " --> pdb=" O SER B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 931 Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 980 through 993 Processing helix chain 'B' and resid 1008 through 1013 Processing helix chain 'C' and resid 95 through 109 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 191 through 195 Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 211 through 220 Processing helix chain 'C' and resid 230 through 240 removed outlier: 4.444A pdb=" N ALA C 234 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 Processing helix chain 'C' and resid 258 through 267 removed outlier: 3.508A pdb=" N GLU C 262 " --> pdb=" O CYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 271 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 314 through 328 Processing helix chain 'C' and resid 330 through 335 Processing helix chain 'C' and resid 337 through 345 removed outlier: 3.532A pdb=" N CYS C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 374 removed outlier: 3.739A pdb=" N ASN C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 382 through 403 Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'C' and resid 415 through 417 No H-bonds generated for 'chain 'C' and resid 415 through 417' Processing helix chain 'C' and resid 418 through 425 Processing helix chain 'C' and resid 443 through 460 Processing helix chain 'C' and resid 463 through 475 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'C' and resid 487 through 498 removed outlier: 3.679A pdb=" N SER C 498 " --> pdb=" O THR C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 511 Processing helix chain 'C' and resid 541 through 565 Processing helix chain 'C' and resid 573 through 580 removed outlier: 3.697A pdb=" N ALA C 577 " --> pdb=" O GLN C 573 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 578 " --> pdb=" O GLU C 574 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 579 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 removed outlier: 4.255A pdb=" N PHE C 596 " --> pdb=" O PRO C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 609 Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.573A pdb=" N VAL C 649 " --> pdb=" O PRO C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 686 removed outlier: 3.754A pdb=" N SER C 686 " --> pdb=" O LYS C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 709 Processing helix chain 'C' and resid 725 through 735 Processing helix chain 'C' and resid 778 through 788 removed outlier: 4.229A pdb=" N LYS C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 815 Processing helix chain 'C' and resid 833 through 843 Processing helix chain 'C' and resid 844 through 846 No H-bonds generated for 'chain 'C' and resid 844 through 846' Processing helix chain 'C' and resid 863 through 873 Processing helix chain 'C' and resid 891 through 894 Processing helix chain 'C' and resid 895 through 904 removed outlier: 3.559A pdb=" N LEU C 900 " --> pdb=" O LEU C 896 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS C 901 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N HIS C 902 " --> pdb=" O SER C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 931 Processing helix chain 'C' and resid 954 through 958 Processing helix chain 'C' and resid 980 through 993 Processing helix chain 'C' and resid 1008 through 1015 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 430 Processing sheet with id=AA4, first strand: chain 'A' and resid 583 through 587 removed outlier: 6.062A pdb=" N ILE A 612 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR A 665 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 614 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU A 662 " --> pdb=" O ARG A 691 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLN A 693 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 664 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LYS A 695 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU A 666 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU A 690 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N MET A 718 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 692 " --> pdb=" O MET A 718 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLU A 720 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 694 " --> pdb=" O GLU A 720 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 768 " --> pdb=" O HIS A 797 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N THR A 799 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET A 770 " --> pdb=" O THR A 799 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE A 796 " --> pdb=" O GLN A 826 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL A 828 " --> pdb=" O PHE A 796 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 798 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 859 through 860 Processing sheet with id=AA6, first strand: chain 'A' and resid 884 through 886 removed outlier: 3.561A pdb=" N LEU A 884 " --> pdb=" O LYS A 911 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AA8, first strand: chain 'B' and resid 151 through 153 Processing sheet with id=AA9, first strand: chain 'B' and resid 427 through 430 Processing sheet with id=AB1, first strand: chain 'B' and resid 583 through 587 removed outlier: 6.724A pdb=" N ARG B 660 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N THR B 688 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N SER B 716 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU B 690 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N MET B 718 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 692 " --> pdb=" O MET B 718 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLU B 720 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE B 694 " --> pdb=" O GLU B 720 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 801 " --> pdb=" O ASN B 772 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE B 796 " --> pdb=" O GLN B 826 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL B 828 " --> pdb=" O PHE B 796 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 798 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 859 through 860 Processing sheet with id=AB3, first strand: chain 'B' and resid 884 through 885 removed outlier: 7.326A pdb=" N LEU B 884 " --> pdb=" O GLY B 913 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 943 " --> pdb=" O LEU B 912 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1000 through 1001 removed outlier: 8.094A pdb=" N ALA B1000 " --> pdb=" O VAL B1022 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AB6, first strand: chain 'C' and resid 151 through 153 removed outlier: 6.472A pdb=" N CYS C 165 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N THR C 279 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE C 167 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 427 through 430 Processing sheet with id=AB8, first strand: chain 'C' and resid 583 through 587 removed outlier: 6.250A pdb=" N LEU C 662 " --> pdb=" O ARG C 691 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLN C 693 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 664 " --> pdb=" O GLN C 693 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU C 690 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 716 " --> pdb=" O LEU C 690 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 859 through 860 Processing sheet with id=AC1, first strand: chain 'C' and resid 884 through 885 removed outlier: 7.209A pdb=" N LEU C 884 " --> pdb=" O GLY C 913 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 943 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1000 through 1001 removed outlier: 8.053A pdb=" N ALA C1000 " --> pdb=" O VAL C1022 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 931 hydrogen bonds defined for protein. 2601 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: 8.19 Time building geometry restraints manager: 8.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3684 1.31 - 1.44: 5530 1.44 - 1.57: 12627 1.57 - 1.71: 8 1.71 - 1.84: 162 Bond restraints: 22011 Sorted by residual: bond pdb=" N ALA A 307 " pdb=" CA ALA A 307 " ideal model delta sigma weight residual 1.459 1.412 0.047 1.21e-02 6.83e+03 1.49e+01 bond pdb=" CD GLU A 729 " pdb=" OE1 GLU A 729 " ideal model delta sigma weight residual 1.249 1.176 0.073 1.90e-02 2.77e+03 1.46e+01 bond pdb=" CD GLU A 729 " pdb=" OE2 GLU A 729 " ideal model delta sigma weight residual 1.249 1.177 0.072 1.90e-02 2.77e+03 1.43e+01 bond pdb=" CB ILE C 644 " pdb=" CG1 ILE C 644 " ideal model delta sigma weight residual 1.530 1.604 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" N ALA A 548 " pdb=" CA ALA A 548 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.21e-02 6.83e+03 1.26e+01 ... (remaining 22006 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.42: 432 106.42 - 113.31: 12182 113.31 - 120.20: 7517 120.20 - 127.09: 9407 127.09 - 133.98: 159 Bond angle restraints: 29697 Sorted by residual: angle pdb=" C ILE B 223 " pdb=" N PRO B 224 " pdb=" CA PRO B 224 " ideal model delta sigma weight residual 119.89 128.09 -8.20 1.02e+00 9.61e-01 6.46e+01 angle pdb=" C LYS B 254 " pdb=" N PRO B 255 " pdb=" CA PRO B 255 " ideal model delta sigma weight residual 119.56 127.51 -7.95 1.02e+00 9.61e-01 6.07e+01 angle pdb=" C GLU A 818 " pdb=" N PRO A 819 " pdb=" CA PRO A 819 " ideal model delta sigma weight residual 119.90 127.65 -7.75 1.02e+00 9.61e-01 5.77e+01 angle pdb=" C LEU A 602 " pdb=" N PRO A 603 " pdb=" CA PRO A 603 " ideal model delta sigma weight residual 120.03 127.36 -7.33 9.90e-01 1.02e+00 5.48e+01 angle pdb=" C ILE A 591 " pdb=" N PRO A 592 " pdb=" CA PRO A 592 " ideal model delta sigma weight residual 119.78 127.22 -7.44 1.03e+00 9.43e-01 5.22e+01 ... (remaining 29692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 12771 17.37 - 34.74: 409 34.74 - 52.10: 76 52.10 - 69.47: 37 69.47 - 86.84: 24 Dihedral angle restraints: 13317 sinusoidal: 5427 harmonic: 7890 Sorted by residual: dihedral pdb=" CA SER B 163 " pdb=" C SER B 163 " pdb=" N PRO B 164 " pdb=" CA PRO B 164 " ideal model delta harmonic sigma weight residual -180.00 -142.63 -37.37 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CA SER C 163 " pdb=" C SER C 163 " pdb=" N PRO C 164 " pdb=" CA PRO C 164 " ideal model delta harmonic sigma weight residual -180.00 -144.66 -35.34 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA SER A 163 " pdb=" C SER A 163 " pdb=" N PRO A 164 " pdb=" CA PRO A 164 " ideal model delta harmonic sigma weight residual -180.00 -146.31 -33.69 0 5.00e+00 4.00e-02 4.54e+01 ... (remaining 13314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2339 0.065 - 0.129: 798 0.129 - 0.194: 254 0.194 - 0.258: 24 0.258 - 0.323: 5 Chirality restraints: 3420 Sorted by residual: chirality pdb=" CA ALA A 307 " pdb=" N ALA A 307 " pdb=" C ALA A 307 " pdb=" CB ALA A 307 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ALA A 548 " pdb=" N ALA A 548 " pdb=" C ALA A 548 " pdb=" CB ALA A 548 " both_signs ideal model delta sigma weight residual False 2.48 2.77 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ILE C 223 " pdb=" N ILE C 223 " pdb=" C ILE C 223 " pdb=" CB ILE C 223 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 3417 not shown) Planarity restraints: 3765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B1024 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ALA B1024 " 0.063 2.00e-02 2.50e+03 pdb=" O ALA B1024 " -0.022 2.00e-02 2.50e+03 pdb=" OXT ALA B1024 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 954 " 0.034 2.00e-02 2.50e+03 1.82e-02 8.30e+00 pdb=" CG TRP C 954 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP C 954 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP C 954 " -0.031 2.00e-02 2.50e+03 pdb=" NE1 TRP C 954 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 954 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 954 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 954 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 954 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 954 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 917 " 0.034 2.00e-02 2.50e+03 1.75e-02 7.69e+00 pdb=" CG TRP A 917 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 917 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 917 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 917 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 917 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 917 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 917 " 0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 917 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 917 " 0.010 2.00e-02 2.50e+03 ... (remaining 3762 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 7239 2.84 - 3.36: 20986 3.36 - 3.87: 35034 3.87 - 4.39: 42648 4.39 - 4.90: 67836 Nonbonded interactions: 173743 Sorted by model distance: nonbonded pdb=" OG SER A 485 " pdb=" N THR A 486 " model vdw 2.330 2.520 nonbonded pdb=" OG SER B 485 " pdb=" N THR B 486 " model vdw 2.347 2.520 nonbonded pdb=" NZ LYS C 175 " pdb=" OD2 ASP C 248 " model vdw 2.354 2.520 nonbonded pdb=" O SER A 481 " pdb=" OG SER A 485 " model vdw 2.356 2.440 nonbonded pdb=" O SER B 481 " pdb=" OG SER B 485 " model vdw 2.359 2.440 ... (remaining 173738 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' selection = chain 'C' } 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 group one per residue 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: 6.080 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: 0.020 Extract box with map and model: 23.450 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 57.310 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.110 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.012 0.085 22011 Z= 0.759 Angle : 1.195 12.072 29697 Z= 0.825 Chirality : 0.070 0.323 3420 Planarity : 0.005 0.036 3765 Dihedral : 10.840 86.838 8187 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.07 % Favored : 94.07 % Rotamer: Outliers : 0.08 % Allowed : 0.66 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 4.55 % 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: -0.82 (0.16), residues: 2700 helix: -0.15 (0.14), residues: 1206 sheet: -0.22 (0.27), residues: 339 loop : -0.94 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.007 TRP A 917 HIS 0.004 0.001 HIS A 797 PHE 0.020 0.003 PHE C 957 TYR 0.031 0.004 TYR B 449 ARG 0.002 0.000 ARG C 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 648 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.9586 (tp) cc_final: 0.9186 (tp) REVERT: A 223 ILE cc_start: 0.7190 (mt) cc_final: 0.6753 (mm) REVERT: A 232 PHE cc_start: 0.9100 (t80) cc_final: 0.8867 (t80) REVERT: A 233 MET cc_start: 0.9092 (mmt) cc_final: 0.8280 (mmm) REVERT: A 353 GLU cc_start: 0.8055 (tp30) cc_final: 0.7559 (mp0) REVERT: A 408 PHE cc_start: 0.8728 (m-80) cc_final: 0.8418 (m-10) REVERT: A 513 TYR cc_start: 0.7704 (p90) cc_final: 0.7320 (p90) REVERT: A 584 LEU cc_start: 0.9252 (tp) cc_final: 0.9041 (tt) REVERT: A 659 PHE cc_start: 0.8894 (m-80) cc_final: 0.8435 (m-10) REVERT: A 716 SER cc_start: 0.9137 (t) cc_final: 0.8439 (m) REVERT: A 740 THR cc_start: 0.8431 (m) cc_final: 0.8231 (p) REVERT: A 793 MET cc_start: 0.6809 (mmm) cc_final: 0.6587 (mmm) REVERT: A 831 CYS cc_start: 0.8325 (m) cc_final: 0.8015 (m) REVERT: A 941 GLN cc_start: 0.8127 (mp10) cc_final: 0.7661 (mm-40) REVERT: B 197 PHE cc_start: 0.8763 (m-80) cc_final: 0.8466 (m-10) REVERT: B 220 LEU cc_start: 0.9250 (mt) cc_final: 0.9000 (mt) REVERT: B 241 GLN cc_start: 0.8127 (mt0) cc_final: 0.7889 (pm20) REVERT: B 574 GLU cc_start: 0.8591 (mp0) cc_final: 0.8178 (mp0) REVERT: B 729 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8545 (tp30) REVERT: B 768 LEU cc_start: 0.9119 (tp) cc_final: 0.8724 (tp) REVERT: B 770 MET cc_start: 0.7500 (tmm) cc_final: 0.7067 (tmm) REVERT: B 796 PHE cc_start: 0.8730 (t80) cc_final: 0.8455 (t80) REVERT: B 885 MET cc_start: 0.6964 (mmp) cc_final: 0.6653 (mmp) REVERT: B 954 TRP cc_start: 0.7003 (m-90) cc_final: 0.6452 (m-90) REVERT: B 1002 LEU cc_start: 0.9137 (tp) cc_final: 0.8139 (tp) REVERT: B 1005 TRP cc_start: 0.8175 (m100) cc_final: 0.7169 (m100) REVERT: B 1008 ASP cc_start: 0.9284 (t0) cc_final: 0.8985 (m-30) REVERT: C 106 LYS cc_start: 0.9020 (mttt) cc_final: 0.8606 (mmmt) REVERT: C 115 LEU cc_start: 0.9158 (mt) cc_final: 0.8776 (mm) REVERT: C 122 GLU cc_start: 0.8148 (mp0) cc_final: 0.7869 (tp30) REVERT: C 212 LEU cc_start: 0.9231 (tp) cc_final: 0.8650 (tp) REVERT: C 244 LEU cc_start: 0.9244 (mt) cc_final: 0.8853 (mp) REVERT: C 444 LYS cc_start: 0.9191 (mttt) cc_final: 0.8953 (tttm) REVERT: C 571 LEU cc_start: 0.9482 (mt) cc_final: 0.9275 (mm) REVERT: C 585 TYR cc_start: 0.8885 (t80) cc_final: 0.8113 (t80) REVERT: C 615 ASP cc_start: 0.8211 (t0) cc_final: 0.7773 (m-30) REVERT: C 792 LYS cc_start: 0.7283 (mttt) cc_final: 0.6940 (ttpp) REVERT: C 823 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7296 (mm-30) REVERT: C 826 GLN cc_start: 0.7690 (mt0) cc_final: 0.7437 (tp40) REVERT: C 944 LEU cc_start: 0.8227 (tt) cc_final: 0.8027 (tt) outliers start: 2 outliers final: 1 residues processed: 650 average time/residue: 0.3691 time to fit residues: 355.8675 Evaluate side-chains 331 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN A 749 GLN A 797 HIS A 800 HIS ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 HIS B 151 GLN B 155 ASN B 162 GLN B 268 ASN ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 ASN C 147 HIS C 268 ASN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22011 Z= 0.190 Angle : 0.638 12.252 29697 Z= 0.336 Chirality : 0.040 0.199 3420 Planarity : 0.004 0.060 3765 Dihedral : 4.908 40.495 2871 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.78 % Favored : 94.11 % Rotamer: Outliers : 0.12 % Allowed : 1.73 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 4.55 % Twisted General : 0.04 % 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: -0.01 (0.17), residues: 2700 helix: 1.11 (0.15), residues: 1182 sheet: 0.09 (0.28), residues: 312 loop : -1.16 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 186 HIS 0.005 0.001 HIS A 744 PHE 0.024 0.002 PHE A 957 TYR 0.017 0.001 TYR C 594 ARG 0.009 0.001 ARG C 691 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 430 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.9256 (tmm) cc_final: 0.9038 (tmm) REVERT: A 233 MET cc_start: 0.8965 (mmt) cc_final: 0.8320 (mmm) REVERT: A 309 ILE cc_start: 0.9576 (mt) cc_final: 0.9297 (tp) REVERT: A 513 TYR cc_start: 0.7772 (p90) cc_final: 0.7568 (p90) REVERT: A 571 LEU cc_start: 0.9390 (mm) cc_final: 0.9151 (mm) REVERT: A 755 LEU cc_start: 0.9246 (pp) cc_final: 0.8912 (tt) REVERT: A 793 MET cc_start: 0.6932 (mmm) cc_final: 0.6304 (mmm) REVERT: A 881 LEU cc_start: 0.8032 (mt) cc_final: 0.7829 (pt) REVERT: B 114 PHE cc_start: 0.8377 (t80) cc_final: 0.8162 (t80) REVERT: B 155 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7514 (t0) REVERT: B 158 LEU cc_start: 0.8489 (mp) cc_final: 0.7871 (tp) REVERT: B 185 LEU cc_start: 0.9665 (mt) cc_final: 0.9170 (mt) REVERT: B 321 LEU cc_start: 0.9307 (mt) cc_final: 0.8983 (tt) REVERT: B 480 ILE cc_start: 0.9083 (mm) cc_final: 0.8768 (tt) REVERT: B 574 GLU cc_start: 0.8512 (mp0) cc_final: 0.8292 (mp0) REVERT: B 584 LEU cc_start: 0.8993 (tp) cc_final: 0.8756 (tp) REVERT: B 659 PHE cc_start: 0.7590 (m-10) cc_final: 0.6562 (t80) REVERT: B 694 ILE cc_start: 0.9538 (mp) cc_final: 0.9312 (tt) REVERT: B 770 MET cc_start: 0.7277 (tmm) cc_final: 0.6728 (tmm) REVERT: B 796 PHE cc_start: 0.8653 (t80) cc_final: 0.8386 (t80) REVERT: B 808 MET cc_start: 0.5640 (mtt) cc_final: 0.4640 (mpp) REVERT: B 818 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6735 (tp30) REVERT: B 1005 TRP cc_start: 0.8345 (m100) cc_final: 0.7716 (m100) REVERT: C 106 LYS cc_start: 0.9257 (mttt) cc_final: 0.8801 (mmmt) REVERT: C 122 GLU cc_start: 0.8269 (mp0) cc_final: 0.8020 (tp30) REVERT: C 184 MET cc_start: 0.9065 (ttm) cc_final: 0.8857 (tpp) REVERT: C 215 THR cc_start: 0.9304 (m) cc_final: 0.9037 (p) REVERT: C 335 MET cc_start: 0.9280 (mmm) cc_final: 0.9058 (tpp) REVERT: C 337 THR cc_start: 0.9258 (m) cc_final: 0.9010 (p) REVERT: C 401 VAL cc_start: 0.9494 (t) cc_final: 0.9203 (t) REVERT: C 444 LYS cc_start: 0.9260 (mttt) cc_final: 0.8994 (tttp) REVERT: C 487 TYR cc_start: 0.8706 (m-80) cc_final: 0.7973 (m-80) REVERT: C 597 ASP cc_start: 0.9343 (m-30) cc_final: 0.9141 (m-30) REVERT: C 765 LEU cc_start: 0.8134 (tp) cc_final: 0.7911 (tp) REVERT: C 792 LYS cc_start: 0.7220 (mttt) cc_final: 0.6876 (ttpt) REVERT: C 793 MET cc_start: 0.6711 (mmm) cc_final: 0.6460 (mmm) outliers start: 3 outliers final: 0 residues processed: 432 average time/residue: 0.3338 time to fit residues: 232.0237 Evaluate side-chains 283 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 282 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 204 optimal weight: 0.6980 chunk 166 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 243 optimal weight: 0.0040 chunk 83 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 155 ASN A 268 ASN A 273 ASN A 286 HIS ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 744 HIS B 103 GLN B 162 GLN ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN C 550 ASN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22011 Z= 0.239 Angle : 0.659 12.298 29697 Z= 0.344 Chirality : 0.040 0.182 3420 Planarity : 0.004 0.057 3765 Dihedral : 4.936 34.273 2871 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.04 % Allowed : 2.52 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.04 % 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: -0.03 (0.17), residues: 2700 helix: 1.18 (0.16), residues: 1185 sheet: 0.02 (0.29), residues: 309 loop : -1.25 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 917 HIS 0.011 0.001 HIS A 601 PHE 0.023 0.002 PHE B 957 TYR 0.019 0.002 TYR C 594 ARG 0.008 0.001 ARG B 691 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 350 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8037 (pp20) cc_final: 0.7803 (pm20) REVERT: A 184 MET cc_start: 0.9227 (tmm) cc_final: 0.9027 (tmm) REVERT: A 309 ILE cc_start: 0.9672 (mt) cc_final: 0.9437 (tp) REVERT: A 755 LEU cc_start: 0.9248 (pp) cc_final: 0.8965 (tt) REVERT: A 793 MET cc_start: 0.6871 (mmm) cc_final: 0.6505 (mmm) REVERT: A 902 HIS cc_start: 0.8269 (p90) cc_final: 0.7813 (p-80) REVERT: A 958 MET cc_start: 0.7658 (tpt) cc_final: 0.7423 (tpt) REVERT: B 158 LEU cc_start: 0.8627 (mp) cc_final: 0.7967 (tt) REVERT: B 274 MET cc_start: 0.8653 (mmp) cc_final: 0.8386 (mmm) REVERT: B 321 LEU cc_start: 0.9370 (mt) cc_final: 0.9046 (tt) REVERT: B 612 ILE cc_start: 0.7943 (mm) cc_final: 0.7575 (mm) REVERT: B 743 ILE cc_start: 0.9439 (mt) cc_final: 0.9234 (tp) REVERT: B 775 MET cc_start: 0.5369 (mpp) cc_final: 0.4716 (mpp) REVERT: B 796 PHE cc_start: 0.8672 (t80) cc_final: 0.8429 (t80) REVERT: C 106 LYS cc_start: 0.9439 (mttt) cc_final: 0.9066 (mmmt) REVERT: C 122 GLU cc_start: 0.8411 (mp0) cc_final: 0.8036 (tp30) REVERT: C 184 MET cc_start: 0.9107 (ttm) cc_final: 0.8743 (tpp) REVERT: C 317 LEU cc_start: 0.9289 (mt) cc_final: 0.9071 (mt) REVERT: C 335 MET cc_start: 0.9244 (mmm) cc_final: 0.9041 (tpp) REVERT: C 337 THR cc_start: 0.9264 (m) cc_final: 0.8911 (p) REVERT: C 401 VAL cc_start: 0.9613 (t) cc_final: 0.9374 (t) REVERT: C 444 LYS cc_start: 0.9369 (mttt) cc_final: 0.9050 (tttp) REVERT: C 487 TYR cc_start: 0.8840 (m-80) cc_final: 0.8252 (m-80) REVERT: C 571 LEU cc_start: 0.9601 (mm) cc_final: 0.9342 (mt) REVERT: C 597 ASP cc_start: 0.9367 (m-30) cc_final: 0.9120 (m-30) REVERT: C 652 PHE cc_start: 0.9075 (m-80) cc_final: 0.8835 (m-10) REVERT: C 765 LEU cc_start: 0.8082 (tp) cc_final: 0.7635 (tp) REVERT: C 792 LYS cc_start: 0.7452 (mttt) cc_final: 0.7032 (ttpp) REVERT: C 793 MET cc_start: 0.6824 (mmm) cc_final: 0.6595 (mmm) REVERT: C 999 GLU cc_start: 0.8357 (tp30) cc_final: 0.7964 (tp30) REVERT: C 1019 PHE cc_start: 0.7900 (t80) cc_final: 0.7690 (t80) outliers start: 1 outliers final: 1 residues processed: 351 average time/residue: 0.3012 time to fit residues: 169.0021 Evaluate side-chains 246 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 8.9990 chunk 184 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A 573 GLN A 744 HIS B 162 GLN B 772 ASN ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 GLN C 145 HIS C 147 HIS ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22011 Z= 0.206 Angle : 0.631 11.758 29697 Z= 0.326 Chirality : 0.040 0.165 3420 Planarity : 0.004 0.056 3765 Dihedral : 4.917 33.822 2871 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.04 % 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: -0.21 (0.17), residues: 2700 helix: 1.13 (0.16), residues: 1206 sheet: 0.05 (0.28), residues: 306 loop : -1.56 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 954 HIS 0.009 0.001 HIS A 744 PHE 0.021 0.002 PHE C 957 TYR 0.018 0.001 TYR C 594 ARG 0.008 0.001 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8130 (pp20) cc_final: 0.7834 (pm20) REVERT: A 309 ILE cc_start: 0.9668 (mt) cc_final: 0.9351 (tp) REVERT: A 611 PHE cc_start: 0.8290 (m-80) cc_final: 0.8003 (m-10) REVERT: A 755 LEU cc_start: 0.9237 (pp) cc_final: 0.8918 (tt) REVERT: A 770 MET cc_start: 0.8069 (mmm) cc_final: 0.7522 (mmp) REVERT: A 793 MET cc_start: 0.6737 (mmm) cc_final: 0.6299 (mmm) REVERT: A 808 MET cc_start: 0.8083 (tmm) cc_final: 0.7202 (ttp) REVERT: A 875 MET cc_start: 0.7916 (tmm) cc_final: 0.6642 (mtm) REVERT: A 902 HIS cc_start: 0.8163 (p90) cc_final: 0.7271 (t-90) REVERT: A 994 LEU cc_start: 0.8719 (tp) cc_final: 0.8453 (tp) REVERT: A 1010 ASP cc_start: 0.8569 (m-30) cc_final: 0.7931 (p0) REVERT: B 158 LEU cc_start: 0.8688 (mp) cc_final: 0.8034 (tt) REVERT: B 197 PHE cc_start: 0.7945 (m-10) cc_final: 0.7574 (m-10) REVERT: B 274 MET cc_start: 0.8641 (mmp) cc_final: 0.8342 (mmm) REVERT: B 321 LEU cc_start: 0.9387 (mt) cc_final: 0.9080 (tt) REVERT: B 612 ILE cc_start: 0.7993 (mm) cc_final: 0.7615 (mm) REVERT: B 659 PHE cc_start: 0.8221 (m-10) cc_final: 0.7873 (m-10) REVERT: B 743 ILE cc_start: 0.9449 (mt) cc_final: 0.9208 (tp) REVERT: B 808 MET cc_start: 0.6757 (mtm) cc_final: 0.6084 (mpp) REVERT: B 1002 LEU cc_start: 0.9362 (tp) cc_final: 0.8564 (tp) REVERT: B 1005 TRP cc_start: 0.8445 (m100) cc_final: 0.8014 (m100) REVERT: C 122 GLU cc_start: 0.8318 (mp0) cc_final: 0.7987 (tp30) REVERT: C 184 MET cc_start: 0.9119 (ttm) cc_final: 0.8738 (tpp) REVERT: C 317 LEU cc_start: 0.9306 (mt) cc_final: 0.9096 (mt) REVERT: C 401 VAL cc_start: 0.9591 (t) cc_final: 0.9355 (t) REVERT: C 444 LYS cc_start: 0.9473 (mttt) cc_final: 0.9084 (tttp) REVERT: C 487 TYR cc_start: 0.8861 (m-80) cc_final: 0.8314 (m-80) REVERT: C 550 ASN cc_start: 0.8965 (m-40) cc_final: 0.8686 (m-40) REVERT: C 571 LEU cc_start: 0.9586 (mm) cc_final: 0.9346 (mt) REVERT: C 585 TYR cc_start: 0.7903 (t80) cc_final: 0.7437 (t80) REVERT: C 597 ASP cc_start: 0.9325 (m-30) cc_final: 0.9051 (m-30) REVERT: C 615 ASP cc_start: 0.8338 (t0) cc_final: 0.8036 (t70) REVERT: C 765 LEU cc_start: 0.8049 (tp) cc_final: 0.7633 (tp) REVERT: C 792 LYS cc_start: 0.7498 (mttt) cc_final: 0.7064 (ttpt) REVERT: C 793 MET cc_start: 0.6743 (mmm) cc_final: 0.6404 (mmm) REVERT: C 795 LEU cc_start: 0.8596 (mp) cc_final: 0.8331 (tt) REVERT: C 970 PHE cc_start: 0.9451 (p90) cc_final: 0.9237 (p90) REVERT: C 999 GLU cc_start: 0.8361 (tp30) cc_final: 0.7931 (tp30) REVERT: C 1019 PHE cc_start: 0.7902 (t80) cc_final: 0.7642 (t80) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.3007 time to fit residues: 152.0000 Evaluate side-chains 233 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 194 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 234 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 180 GLN A 273 ASN A 348 GLN A 357 HIS ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS C 374 ASN C 508 HIS ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22011 Z= 0.154 Angle : 0.591 11.411 29697 Z= 0.303 Chirality : 0.039 0.180 3420 Planarity : 0.003 0.049 3765 Dihedral : 4.737 32.053 2871 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % Twisted General : 0.04 % 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: 0.01 (0.17), residues: 2700 helix: 1.42 (0.16), residues: 1185 sheet: 0.06 (0.29), residues: 303 loop : -1.48 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 888 HIS 0.004 0.001 HIS A 601 PHE 0.022 0.001 PHE C 957 TYR 0.017 0.001 TYR C 594 ARG 0.006 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ILE cc_start: 0.9581 (mt) cc_final: 0.9370 (tp) REVERT: A 611 PHE cc_start: 0.8332 (m-80) cc_final: 0.8062 (m-10) REVERT: A 755 LEU cc_start: 0.9286 (pp) cc_final: 0.8990 (tt) REVERT: A 770 MET cc_start: 0.8197 (mmm) cc_final: 0.7840 (mmp) REVERT: A 793 MET cc_start: 0.6701 (mmm) cc_final: 0.6224 (mmm) REVERT: A 808 MET cc_start: 0.8105 (tmm) cc_final: 0.7377 (ttp) REVERT: A 875 MET cc_start: 0.7809 (tmm) cc_final: 0.6595 (mtm) REVERT: A 902 HIS cc_start: 0.8231 (p90) cc_final: 0.7229 (t-90) REVERT: A 994 LEU cc_start: 0.8742 (tp) cc_final: 0.8453 (tp) REVERT: A 1010 ASP cc_start: 0.8543 (m-30) cc_final: 0.7922 (p0) REVERT: B 158 LEU cc_start: 0.8634 (mp) cc_final: 0.8017 (tp) REVERT: B 197 PHE cc_start: 0.7960 (m-10) cc_final: 0.7420 (m-80) REVERT: B 274 MET cc_start: 0.8487 (mmp) cc_final: 0.8243 (mmm) REVERT: B 321 LEU cc_start: 0.9176 (mt) cc_final: 0.8958 (tt) REVERT: B 562 TYR cc_start: 0.8778 (t80) cc_final: 0.8370 (t80) REVERT: B 612 ILE cc_start: 0.7997 (mm) cc_final: 0.7776 (mm) REVERT: B 714 ILE cc_start: 0.8447 (pt) cc_final: 0.8223 (tp) REVERT: B 717 LEU cc_start: 0.9524 (mm) cc_final: 0.9220 (mm) REVERT: B 770 MET cc_start: 0.7077 (tmm) cc_final: 0.6813 (tmm) REVERT: B 808 MET cc_start: 0.6741 (mtm) cc_final: 0.6086 (mpp) REVERT: B 885 MET cc_start: 0.8318 (tpt) cc_final: 0.8115 (tpp) REVERT: B 970 PHE cc_start: 0.8077 (p90) cc_final: 0.7728 (p90) REVERT: B 1002 LEU cc_start: 0.9321 (tp) cc_final: 0.8613 (tp) REVERT: B 1005 TRP cc_start: 0.8530 (m-10) cc_final: 0.8162 (m100) REVERT: C 184 MET cc_start: 0.9108 (ttm) cc_final: 0.8739 (tpp) REVERT: C 401 VAL cc_start: 0.9573 (t) cc_final: 0.9304 (t) REVERT: C 444 LYS cc_start: 0.9495 (mttt) cc_final: 0.9019 (tptp) REVERT: C 487 TYR cc_start: 0.8786 (m-80) cc_final: 0.8218 (m-80) REVERT: C 597 ASP cc_start: 0.9244 (m-30) cc_final: 0.8988 (m-30) REVERT: C 765 LEU cc_start: 0.8063 (tp) cc_final: 0.7806 (tp) REVERT: C 792 LYS cc_start: 0.7400 (mttt) cc_final: 0.6938 (ttpt) REVERT: C 795 LEU cc_start: 0.8588 (mp) cc_final: 0.8318 (tt) REVERT: C 875 MET cc_start: 0.8434 (pmm) cc_final: 0.8207 (pmm) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.3222 time to fit residues: 165.5355 Evaluate side-chains 237 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 0.0470 chunk 235 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 153 optimal weight: 0.0000 chunk 64 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 137 optimal weight: 0.0470 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS A 744 HIS B 162 GLN B 471 ASN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 147 HIS C 357 HIS ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22011 Z= 0.130 Angle : 0.584 11.661 29697 Z= 0.294 Chirality : 0.039 0.152 3420 Planarity : 0.003 0.047 3765 Dihedral : 4.519 30.700 2871 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.10 (0.17), residues: 2700 helix: 1.53 (0.16), residues: 1185 sheet: -0.04 (0.30), residues: 297 loop : -1.43 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 888 HIS 0.009 0.001 HIS A 744 PHE 0.023 0.001 PHE C 957 TYR 0.015 0.001 TYR C 594 ARG 0.005 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ILE cc_start: 0.9596 (mt) cc_final: 0.9376 (tp) REVERT: A 611 PHE cc_start: 0.8302 (m-80) cc_final: 0.8067 (m-10) REVERT: A 755 LEU cc_start: 0.9253 (pp) cc_final: 0.8955 (tt) REVERT: A 770 MET cc_start: 0.8101 (mmm) cc_final: 0.7791 (mmp) REVERT: A 793 MET cc_start: 0.6643 (mmm) cc_final: 0.6203 (mmm) REVERT: A 808 MET cc_start: 0.7942 (tmm) cc_final: 0.7249 (ttp) REVERT: A 826 GLN cc_start: 0.8949 (mp10) cc_final: 0.8694 (mp10) REVERT: A 902 HIS cc_start: 0.8131 (p90) cc_final: 0.7901 (p-80) REVERT: A 994 LEU cc_start: 0.8791 (tp) cc_final: 0.8509 (tp) REVERT: A 1010 ASP cc_start: 0.8498 (m-30) cc_final: 0.7888 (p0) REVERT: B 158 LEU cc_start: 0.8535 (mp) cc_final: 0.7930 (tp) REVERT: B 184 MET cc_start: 0.9366 (ppp) cc_final: 0.9129 (ppp) REVERT: B 197 PHE cc_start: 0.7942 (m-10) cc_final: 0.7381 (m-80) REVERT: B 335 MET cc_start: 0.8414 (mmm) cc_final: 0.8162 (tmm) REVERT: B 340 PHE cc_start: 0.8665 (m-80) cc_final: 0.8420 (m-80) REVERT: B 612 ILE cc_start: 0.7831 (mm) cc_final: 0.7605 (mm) REVERT: B 714 ILE cc_start: 0.8435 (pt) cc_final: 0.8163 (tp) REVERT: B 717 LEU cc_start: 0.9556 (mm) cc_final: 0.9211 (mm) REVERT: B 770 MET cc_start: 0.7167 (tmm) cc_final: 0.6899 (tmm) REVERT: B 775 MET cc_start: 0.5701 (mpp) cc_final: 0.4878 (mpp) REVERT: B 808 MET cc_start: 0.6605 (mtm) cc_final: 0.5967 (mpp) REVERT: B 1002 LEU cc_start: 0.9390 (tp) cc_final: 0.8733 (tp) REVERT: B 1005 TRP cc_start: 0.8611 (m-10) cc_final: 0.8119 (m100) REVERT: C 184 MET cc_start: 0.9083 (ttm) cc_final: 0.8689 (tpp) REVERT: C 215 THR cc_start: 0.9338 (m) cc_final: 0.9132 (p) REVERT: C 444 LYS cc_start: 0.9497 (mttt) cc_final: 0.9277 (tttp) REVERT: C 487 TYR cc_start: 0.8876 (m-80) cc_final: 0.8163 (m-80) REVERT: C 550 ASN cc_start: 0.8981 (m-40) cc_final: 0.8721 (m-40) REVERT: C 571 LEU cc_start: 0.9603 (mm) cc_final: 0.9375 (mt) REVERT: C 597 ASP cc_start: 0.9160 (m-30) cc_final: 0.8893 (m-30) REVERT: C 765 LEU cc_start: 0.7431 (tp) cc_final: 0.7121 (tp) REVERT: C 792 LYS cc_start: 0.7511 (mttt) cc_final: 0.7075 (ttpt) REVERT: C 795 LEU cc_start: 0.8579 (mp) cc_final: 0.8324 (tt) REVERT: C 886 LEU cc_start: 0.8570 (mm) cc_final: 0.8125 (mp) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.3019 time to fit residues: 159.8712 Evaluate side-chains 240 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 147 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS B 162 GLN B 286 HIS B 357 HIS B 447 GLN B 471 ASN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS C 147 HIS C 162 GLN C 348 GLN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22011 Z= 0.261 Angle : 0.669 12.314 29697 Z= 0.347 Chirality : 0.041 0.184 3420 Planarity : 0.004 0.049 3765 Dihedral : 4.929 31.409 2871 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.29 (0.17), residues: 2700 helix: 1.09 (0.16), residues: 1188 sheet: 0.02 (0.30), residues: 273 loop : -1.55 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 888 HIS 0.008 0.001 HIS A 269 PHE 0.023 0.002 PHE C 659 TYR 0.020 0.002 TYR B 487 ARG 0.007 0.001 ARG C 691 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 PHE cc_start: 0.9164 (t80) cc_final: 0.8923 (t80) REVERT: A 309 ILE cc_start: 0.9605 (mt) cc_final: 0.9375 (tp) REVERT: A 611 PHE cc_start: 0.8511 (m-80) cc_final: 0.8131 (m-10) REVERT: A 755 LEU cc_start: 0.9238 (pp) cc_final: 0.8944 (tt) REVERT: A 770 MET cc_start: 0.8275 (mmm) cc_final: 0.7847 (mmp) REVERT: A 793 MET cc_start: 0.6642 (mmm) cc_final: 0.6086 (mmm) REVERT: A 808 MET cc_start: 0.8202 (tmm) cc_final: 0.7533 (ttp) REVERT: A 875 MET cc_start: 0.8249 (tmm) cc_final: 0.6482 (mtm) REVERT: A 902 HIS cc_start: 0.8190 (p90) cc_final: 0.7412 (t-90) REVERT: A 994 LEU cc_start: 0.8788 (tp) cc_final: 0.8499 (tp) REVERT: A 1010 ASP cc_start: 0.8738 (m-30) cc_final: 0.8230 (p0) REVERT: B 158 LEU cc_start: 0.8592 (mp) cc_final: 0.8010 (tp) REVERT: B 184 MET cc_start: 0.9337 (ppp) cc_final: 0.9123 (ppp) REVERT: B 487 TYR cc_start: 0.9242 (m-80) cc_final: 0.8984 (m-80) REVERT: B 612 ILE cc_start: 0.7831 (mm) cc_final: 0.7598 (mm) REVERT: B 775 MET cc_start: 0.6495 (mpp) cc_final: 0.5918 (mpp) REVERT: C 184 MET cc_start: 0.9180 (ttm) cc_final: 0.8783 (tpp) REVERT: C 317 LEU cc_start: 0.9299 (mt) cc_final: 0.9049 (mt) REVERT: C 487 TYR cc_start: 0.9064 (m-80) cc_final: 0.8205 (m-80) REVERT: C 550 ASN cc_start: 0.9053 (m-40) cc_final: 0.8767 (m-40) REVERT: C 571 LEU cc_start: 0.9657 (mm) cc_final: 0.9453 (mt) REVERT: C 597 ASP cc_start: 0.9240 (m-30) cc_final: 0.8960 (m-30) REVERT: C 659 PHE cc_start: 0.8572 (m-10) cc_final: 0.8331 (m-10) REVERT: C 749 GLN cc_start: 0.4810 (mt0) cc_final: 0.4337 (pt0) REVERT: C 765 LEU cc_start: 0.7595 (tp) cc_final: 0.7261 (tp) REVERT: C 792 LYS cc_start: 0.7534 (mttt) cc_final: 0.7045 (ttpt) REVERT: C 875 MET cc_start: 0.8259 (pmm) cc_final: 0.7917 (pmm) REVERT: C 1019 PHE cc_start: 0.8047 (t80) cc_final: 0.7815 (t80) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.2994 time to fit residues: 138.1382 Evaluate side-chains 207 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22011 Z= 0.176 Angle : 0.609 12.658 29697 Z= 0.312 Chirality : 0.040 0.178 3420 Planarity : 0.003 0.050 3765 Dihedral : 4.785 33.238 2871 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.19 (0.17), residues: 2700 helix: 1.26 (0.16), residues: 1188 sheet: -0.17 (0.28), residues: 315 loop : -1.59 (0.19), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 888 HIS 0.005 0.001 HIS A 269 PHE 0.022 0.001 PHE C 957 TYR 0.017 0.001 TYR C 594 ARG 0.006 0.000 ARG C 691 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ILE cc_start: 0.9637 (mt) cc_final: 0.9372 (tp) REVERT: A 611 PHE cc_start: 0.8416 (m-80) cc_final: 0.8067 (m-10) REVERT: A 755 LEU cc_start: 0.9231 (pp) cc_final: 0.8934 (tt) REVERT: A 770 MET cc_start: 0.8266 (mmm) cc_final: 0.7806 (mmp) REVERT: A 793 MET cc_start: 0.6623 (mmm) cc_final: 0.6078 (mmm) REVERT: A 808 MET cc_start: 0.8132 (tmm) cc_final: 0.7492 (ttp) REVERT: A 875 MET cc_start: 0.8177 (tmm) cc_final: 0.7223 (mtm) REVERT: A 902 HIS cc_start: 0.8180 (p90) cc_final: 0.7341 (p90) REVERT: A 994 LEU cc_start: 0.8814 (tp) cc_final: 0.8534 (tp) REVERT: A 1010 ASP cc_start: 0.8681 (m-30) cc_final: 0.8196 (p0) REVERT: B 158 LEU cc_start: 0.8549 (mp) cc_final: 0.8032 (tp) REVERT: B 184 MET cc_start: 0.9308 (ppp) cc_final: 0.9075 (ppp) REVERT: B 487 TYR cc_start: 0.9260 (m-80) cc_final: 0.8955 (m-80) REVERT: B 562 TYR cc_start: 0.8894 (t80) cc_final: 0.8568 (t80) REVERT: B 770 MET cc_start: 0.7112 (tmm) cc_final: 0.6810 (tmm) REVERT: C 106 LYS cc_start: 0.9458 (mttt) cc_final: 0.9035 (tttt) REVERT: C 184 MET cc_start: 0.9167 (ttm) cc_final: 0.8768 (tpp) REVERT: C 235 MET cc_start: 0.9240 (ptp) cc_final: 0.9016 (ptt) REVERT: C 487 TYR cc_start: 0.9013 (m-80) cc_final: 0.8193 (m-80) REVERT: C 550 ASN cc_start: 0.9035 (m-40) cc_final: 0.8757 (m110) REVERT: C 597 ASP cc_start: 0.9235 (m-30) cc_final: 0.8969 (m-30) REVERT: C 795 LEU cc_start: 0.8618 (mp) cc_final: 0.8351 (tt) REVERT: C 875 MET cc_start: 0.8213 (pmm) cc_final: 0.7923 (pmm) REVERT: C 969 PHE cc_start: 0.9287 (p90) cc_final: 0.9087 (p90) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.3011 time to fit residues: 138.2888 Evaluate side-chains 217 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 219 optimal weight: 0.5980 chunk 229 optimal weight: 0.9980 chunk 241 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS ** C 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22011 Z= 0.139 Angle : 0.592 11.188 29697 Z= 0.300 Chirality : 0.040 0.168 3420 Planarity : 0.003 0.043 3765 Dihedral : 4.636 28.550 2871 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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 (0.17), residues: 2700 helix: 1.41 (0.16), residues: 1185 sheet: -0.41 (0.28), residues: 345 loop : -1.48 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 954 HIS 0.004 0.001 HIS A 601 PHE 0.021 0.001 PHE C 659 TYR 0.018 0.001 TYR C 594 ARG 0.005 0.000 ARG C 925 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ILE cc_start: 0.9606 (mt) cc_final: 0.9225 (tp) REVERT: A 611 PHE cc_start: 0.8411 (m-80) cc_final: 0.8084 (m-10) REVERT: A 755 LEU cc_start: 0.9221 (pp) cc_final: 0.8954 (tt) REVERT: A 770 MET cc_start: 0.8238 (mmm) cc_final: 0.7835 (mmp) REVERT: A 793 MET cc_start: 0.6574 (mmm) cc_final: 0.6058 (mmm) REVERT: A 808 MET cc_start: 0.7964 (tmm) cc_final: 0.7307 (ttp) REVERT: A 875 MET cc_start: 0.8071 (tmm) cc_final: 0.6360 (mtm) REVERT: A 902 HIS cc_start: 0.8146 (p90) cc_final: 0.7353 (t-90) REVERT: A 994 LEU cc_start: 0.8813 (tp) cc_final: 0.8535 (tp) REVERT: B 158 LEU cc_start: 0.8534 (mp) cc_final: 0.8018 (tp) REVERT: B 184 MET cc_start: 0.9272 (ppp) cc_final: 0.9024 (ppp) REVERT: B 197 PHE cc_start: 0.8093 (m-10) cc_final: 0.7779 (m-80) REVERT: B 340 PHE cc_start: 0.8688 (m-80) cc_final: 0.8423 (m-80) REVERT: B 562 TYR cc_start: 0.8829 (t80) cc_final: 0.8516 (t80) REVERT: B 770 MET cc_start: 0.7116 (tmm) cc_final: 0.6872 (tmm) REVERT: B 775 MET cc_start: 0.6183 (mpp) cc_final: 0.5447 (mpp) REVERT: C 106 LYS cc_start: 0.9502 (mttt) cc_final: 0.9101 (mmmt) REVERT: C 184 MET cc_start: 0.9109 (ttm) cc_final: 0.8748 (tpp) REVERT: C 348 GLN cc_start: 0.8375 (mm110) cc_final: 0.7937 (mm-40) REVERT: C 487 TYR cc_start: 0.8990 (m-80) cc_final: 0.8089 (m-80) REVERT: C 550 ASN cc_start: 0.9028 (m-40) cc_final: 0.8727 (m110) REVERT: C 597 ASP cc_start: 0.9171 (m-30) cc_final: 0.8951 (m-30) REVERT: C 795 LEU cc_start: 0.8558 (mp) cc_final: 0.8357 (tt) REVERT: C 875 MET cc_start: 0.8200 (pmm) cc_final: 0.7935 (pmm) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.3154 time to fit residues: 152.1519 Evaluate side-chains 216 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 0.9990 chunk 256 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 214 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS ** C 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22011 Z= 0.135 Angle : 0.587 12.013 29697 Z= 0.295 Chirality : 0.039 0.190 3420 Planarity : 0.003 0.042 3765 Dihedral : 4.536 28.461 2871 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.23 (0.17), residues: 2700 helix: 1.67 (0.16), residues: 1152 sheet: -0.23 (0.28), residues: 330 loop : -1.27 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 954 HIS 0.004 0.001 HIS C 147 PHE 0.023 0.001 PHE C 957 TYR 0.017 0.001 TYR C 594 ARG 0.004 0.000 ARG C 691 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ILE cc_start: 0.9492 (mt) cc_final: 0.9172 (tp) REVERT: A 611 PHE cc_start: 0.8390 (m-80) cc_final: 0.8076 (m-10) REVERT: A 755 LEU cc_start: 0.9211 (pp) cc_final: 0.8941 (tt) REVERT: A 793 MET cc_start: 0.6468 (mmm) cc_final: 0.5970 (mmm) REVERT: A 808 MET cc_start: 0.7924 (tmm) cc_final: 0.7265 (ttp) REVERT: A 994 LEU cc_start: 0.8835 (tp) cc_final: 0.8568 (tp) REVERT: B 184 MET cc_start: 0.9283 (ppp) cc_final: 0.9021 (ppp) REVERT: B 197 PHE cc_start: 0.8056 (m-10) cc_final: 0.7697 (m-80) REVERT: B 562 TYR cc_start: 0.8872 (t80) cc_final: 0.8527 (t80) REVERT: B 770 MET cc_start: 0.7054 (tmm) cc_final: 0.6811 (tmm) REVERT: B 775 MET cc_start: 0.5958 (mpp) cc_final: 0.5193 (mpp) REVERT: C 106 LYS cc_start: 0.9504 (mttt) cc_final: 0.9085 (tttm) REVERT: C 184 MET cc_start: 0.9083 (ttm) cc_final: 0.8750 (tpp) REVERT: C 235 MET cc_start: 0.9144 (ptp) cc_final: 0.8937 (ptt) REVERT: C 348 GLN cc_start: 0.8437 (mm110) cc_final: 0.7907 (mm-40) REVERT: C 487 TYR cc_start: 0.8934 (m-80) cc_final: 0.8051 (m-80) REVERT: C 550 ASN cc_start: 0.9018 (m-40) cc_final: 0.8715 (m110) REVERT: C 958 MET cc_start: 0.7844 (mmp) cc_final: 0.7248 (mmm) REVERT: C 969 PHE cc_start: 0.9287 (p90) cc_final: 0.9073 (p90) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2890 time to fit residues: 133.9491 Evaluate side-chains 216 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 214 optimal weight: 0.0970 chunk 89 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS B 162 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.081059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.060239 restraints weight = 117460.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.062092 restraints weight = 72254.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.063328 restraints weight = 51961.320| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22011 Z= 0.153 Angle : 0.594 11.784 29697 Z= 0.302 Chirality : 0.039 0.177 3420 Planarity : 0.003 0.041 3765 Dihedral : 4.553 27.321 2871 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.04 % Allowed : 0.29 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.20 (0.17), residues: 2700 helix: 1.66 (0.16), residues: 1149 sheet: 0.03 (0.30), residues: 285 loop : -1.33 (0.19), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 954 HIS 0.011 0.001 HIS A 744 PHE 0.022 0.001 PHE C 659 TYR 0.017 0.001 TYR C 594 ARG 0.006 0.000 ARG B 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4628.42 seconds wall clock time: 85 minutes 46.88 seconds (5146.88 seconds total)