Starting phenix.real_space_refine on Mon Mar 18 17:45:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fw2_29496/03_2024/8fw2_29496_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fw2_29496/03_2024/8fw2_29496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fw2_29496/03_2024/8fw2_29496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fw2_29496/03_2024/8fw2_29496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fw2_29496/03_2024/8fw2_29496_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fw2_29496/03_2024/8fw2_29496_neut.pdb" } resolution = 3.8 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= 0.014 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 197": "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 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 585": "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 TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 854": "OD1" <-> "OD2" Residue "A PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 957": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 197": "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 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 596": "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 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 854": "OD1" <-> "OD2" Residue "B PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1019": "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 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 585": "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 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 ASP 854": "OD1" <-> "OD2" 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 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-5265/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: 11.44, per 1000 atoms: 0.53 Number of scatterers: 21612 At special positions: 0 Unit cell: (216.144, 146.94, 100.488, 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: 8.14 Conformation dependent library (CDL) restraints added in 4.2 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: 150 helices and 16 sheets defined 50.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 95 through 109 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 156 through 160 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 224 through 228 removed outlier: 3.599A pdb=" N ILE A 227 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 removed outlier: 4.175A pdb=" N ALA A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'A' and resid 268 through 271 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 330 through 335 Processing helix chain 'A' and resid 337 through 347 removed outlier: 4.135A pdb=" N THR A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.940A 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 403 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 496 Processing helix chain 'A' and resid 499 through 511 Processing helix chain 'A' and resid 541 through 564 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 592 through 602 removed outlier: 4.169A pdb=" N PHE A 596 " --> pdb=" O PRO A 592 " (cutoff:3.500A) removed outlier: 3.540A 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: 3.819A pdb=" N VAL A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 685 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 725 through 733 Processing helix chain 'A' and resid 778 through 788 Processing helix chain 'A' and resid 808 through 815 removed outlier: 3.586A pdb=" N VAL A 812 " --> pdb=" O MET A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 844 through 846 No H-bonds generated for 'chain 'A' and resid 844 through 846' Processing helix chain 'A' and resid 863 through 873 Processing helix chain 'A' and resid 891 through 894 Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.785A 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 959 through 964 Processing helix chain 'A' and resid 980 through 992 removed outlier: 3.769A pdb=" N SER A 992 " --> pdb=" O SER A 988 " (cutoff:3.500A) 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 156 through 160 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 230 through 240 removed outlier: 4.220A pdb=" N ALA B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 267 Processing helix chain 'B' and resid 267 through 272 removed outlier: 4.359A pdb=" N PHE B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) 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 338 through 347 removed outlier: 4.378A pdb=" N THR B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 removed outlier: 3.813A pdb=" N ASN B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 378 Processing helix chain 'B' and resid 382 through 404 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 496 Processing helix chain 'B' and resid 498 through 511 Processing helix chain 'B' and resid 541 through 564 Processing helix chain 'B' and resid 571 through 580 Processing helix chain 'B' and resid 592 through 602 removed outlier: 4.101A pdb=" N PHE B 596 " --> pdb=" O PRO B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 609 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.512A pdb=" N VAL B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 685 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 787 Processing helix chain 'B' and resid 788 through 790 No H-bonds generated for 'chain 'B' and resid 788 through 790' Processing helix chain 'B' and resid 808 through 815 removed outlier: 3.618A pdb=" N VAL B 812 " --> pdb=" O MET B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 843 Processing helix chain 'B' and resid 844 through 846 No H-bonds generated for 'chain 'B' and resid 844 through 846' 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: 3.912A 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 959 through 964 Processing helix chain 'B' and resid 980 through 992 removed outlier: 3.872A pdb=" N SER B 992 " --> pdb=" O SER B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1015 Processing helix chain 'C' and resid 95 through 109 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 156 through 160 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 224 through 228 removed outlier: 3.836A pdb=" N ILE C 227 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 249 through 253 Processing helix chain 'C' and resid 254 through 257 Processing helix chain 'C' and resid 258 through 267 Processing helix chain 'C' and resid 280 through 287 removed outlier: 4.838A pdb=" N ARG C 285 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 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 347 removed outlier: 3.767A pdb=" N CYS C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 374 removed outlier: 3.781A 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 404 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 496 Processing helix chain 'C' and resid 498 through 511 Processing helix chain 'C' and resid 529 through 533 Processing helix chain 'C' and resid 541 through 564 Processing helix chain 'C' and resid 573 through 580 removed outlier: 3.956A pdb=" N ALA C 577 " --> pdb=" O GLN C 573 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE C 578 " --> pdb=" O GLU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 removed outlier: 4.157A 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: 3.888A pdb=" N VAL C 649 " --> pdb=" O PRO C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 685 Processing helix chain 'C' and resid 703 through 709 Processing helix chain 'C' and resid 725 through 733 Processing helix chain 'C' and resid 778 through 787 Processing helix chain 'C' and resid 788 through 790 No H-bonds generated for 'chain 'C' and resid 788 through 790' Processing helix chain 'C' and resid 808 through 815 removed outlier: 3.640A pdb=" N VAL C 812 " --> pdb=" O MET C 808 " (cutoff:3.500A) 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: 3.947A 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 959 through 964 Processing helix chain 'C' and resid 980 through 992 removed outlier: 3.829A pdb=" N SER C 992 " --> pdb=" O SER C 988 " (cutoff:3.500A) 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 148 through 153 removed outlier: 5.084A pdb=" N GLU A 150 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N THR A 294 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N CYS A 165 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR A 279 " --> pdb=" O CYS A 165 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 167 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA4, first strand: chain 'A' and resid 583 through 587 removed outlier: 6.428A pdb=" N ARG A 660 " --> pdb=" O SER A 689 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ARG A 691 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 662 " --> pdb=" O ARG A 691 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLN A 693 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A 664 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LYS A 695 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 666 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N THR A 688 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N SER A 716 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU A 690 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N MET A 718 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 692 " --> pdb=" O MET A 718 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLU A 720 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 694 " --> pdb=" O GLU A 720 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A 741 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASP A 771 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 743 " --> pdb=" O ASP A 771 " (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 885 removed outlier: 6.959A pdb=" N LEU A 884 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 912 " --> pdb=" O ASN A 943 " (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 148 through 153 removed outlier: 5.096A pdb=" N GLU B 150 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 141 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N THR B 294 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N CYS B 165 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR B 279 " --> pdb=" O CYS B 165 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE B 167 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB1, first strand: chain 'B' and resid 583 through 587 removed outlier: 6.463A pdb=" N ARG B 660 " --> pdb=" O SER B 689 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ARG B 691 " --> pdb=" O ARG B 660 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU B 662 " --> pdb=" O ARG B 691 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLN B 693 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 664 " --> pdb=" O GLN B 693 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LYS B 695 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 666 " --> pdb=" O LYS B 695 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N THR B 688 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N SER B 716 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU B 690 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N MET B 718 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 692 " --> pdb=" O MET B 718 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLU B 720 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE B 694 " --> pdb=" O GLU B 720 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU B 741 " --> pdb=" O ILE B 769 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP B 771 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 743 " --> pdb=" O ASP B 771 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 884 through 885 removed outlier: 7.013A pdb=" N LEU B 884 " --> pdb=" O GLY B 913 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 912 " --> pdb=" O ASN B 943 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AB4, first strand: chain 'C' and resid 148 through 153 removed outlier: 5.160A pdb=" N GLU C 150 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C 141 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR C 294 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS C 165 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR C 279 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 167 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'C' and resid 583 through 587 removed outlier: 6.360A pdb=" N ARG C 660 " --> pdb=" O SER C 689 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ARG C 691 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU C 662 " --> pdb=" O ARG C 691 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLN C 693 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 664 " --> pdb=" O GLN C 693 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LYS C 695 " --> pdb=" O VAL C 664 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 666 " --> pdb=" O LYS C 695 " (cutoff:3.500A) removed outlier: 10.901A pdb=" N THR C 688 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N SER C 716 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 690 " --> pdb=" O SER C 716 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N MET C 718 " --> pdb=" O LEU C 690 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 692 " --> pdb=" O MET C 718 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLU C 720 " --> pdb=" O LEU C 692 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE C 694 " --> pdb=" O GLU C 720 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 884 through 885 removed outlier: 6.908A pdb=" N LEU C 884 " --> pdb=" O GLY C 913 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 912 " --> pdb=" O ASN C 943 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 942 " --> pdb=" O PHE C 969 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 942 hydrogen bonds defined for protein. 2589 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: 8.42 Time building geometry restraints manager: 8.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4224 1.32 - 1.45: 5075 1.45 - 1.57: 12539 1.57 - 1.70: 11 1.70 - 1.82: 162 Bond restraints: 22011 Sorted by residual: bond pdb=" CB ILE C 644 " pdb=" CG1 ILE C 644 " ideal model delta sigma weight residual 1.530 1.605 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB ILE A 644 " pdb=" CG1 ILE A 644 " ideal model delta sigma weight residual 1.530 1.605 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C ALA A 784 " pdb=" O ALA A 784 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.17e-02 7.31e+03 8.99e+00 bond pdb=" C GLU A 818 " pdb=" N PRO A 819 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.27e-02 6.20e+03 8.96e+00 bond pdb=" CA ALA A 432 " pdb=" C ALA A 432 " ideal model delta sigma weight residual 1.533 1.517 0.017 5.60e-03 3.19e+04 8.77e+00 ... (remaining 22006 not shown) Histogram of bond angle deviations from ideal: 97.89 - 105.13: 277 105.13 - 112.37: 11357 112.37 - 119.62: 6959 119.62 - 126.86: 10925 126.86 - 134.10: 179 Bond angle restraints: 29697 Sorted by residual: angle pdb=" C GLU B 818 " pdb=" N PRO B 819 " pdb=" CA PRO B 819 " ideal model delta sigma weight residual 119.89 129.64 -9.75 1.02e+00 9.61e-01 9.15e+01 angle pdb=" C VAL A 906 " pdb=" N PRO A 907 " pdb=" CA PRO A 907 " ideal model delta sigma weight residual 119.56 127.51 -7.95 1.02e+00 9.61e-01 6.08e+01 angle pdb=" C LEU C 886 " pdb=" N PRO C 887 " pdb=" CA PRO C 887 " ideal model delta sigma weight residual 119.78 127.77 -7.99 1.03e+00 9.43e-01 6.02e+01 angle pdb=" C LEU B 602 " pdb=" N PRO B 603 " pdb=" CA PRO B 603 " ideal model delta sigma weight residual 120.03 127.49 -7.46 9.90e-01 1.02e+00 5.67e+01 angle pdb=" C THR C 111 " pdb=" N PRO C 112 " pdb=" CA PRO C 112 " ideal model delta sigma weight residual 119.56 127.17 -7.61 1.02e+00 9.61e-01 5.57e+01 ... (remaining 29692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 12768 17.59 - 35.18: 414 35.18 - 52.77: 71 52.77 - 70.37: 54 70.37 - 87.96: 10 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 -145.96 -34.04 0 5.00e+00 4.00e-02 4.64e+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 -146.07 -33.93 0 5.00e+00 4.00e-02 4.60e+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 -146.27 -33.73 0 5.00e+00 4.00e-02 4.55e+01 ... (remaining 13314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2290 0.066 - 0.132: 881 0.132 - 0.198: 238 0.198 - 0.264: 9 0.264 - 0.330: 2 Chirality restraints: 3420 Sorted by residual: chirality pdb=" CB ILE A 644 " pdb=" CA ILE A 644 " pdb=" CG1 ILE A 644 " pdb=" CG2 ILE A 644 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE C 644 " pdb=" CA ILE C 644 " pdb=" CG1 ILE C 644 " pdb=" CG2 ILE C 644 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU C 751 " pdb=" CB LEU C 751 " pdb=" CD1 LEU C 751 " pdb=" CD2 LEU C 751 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3417 not shown) Planarity restraints: 3765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 917 " -0.034 2.00e-02 2.50e+03 1.67e-02 6.98e+00 pdb=" CG TRP C 917 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP C 917 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP C 917 " 0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP C 917 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 917 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 917 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 917 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 917 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 917 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 818 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C GLU A 818 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU A 818 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 819 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 585 " 0.027 2.00e-02 2.50e+03 1.54e-02 4.77e+00 pdb=" CG TYR C 585 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR C 585 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR C 585 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR C 585 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 585 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 585 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 585 " 0.025 2.00e-02 2.50e+03 ... (remaining 3762 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4223 2.77 - 3.30: 20607 3.30 - 3.83: 33485 3.83 - 4.37: 42489 4.37 - 4.90: 69034 Nonbonded interactions: 169838 Sorted by model distance: nonbonded pdb=" O SER B 481 " pdb=" OG SER B 485 " model vdw 2.235 2.440 nonbonded pdb=" O SER C 481 " pdb=" OG SER C 485 " model vdw 2.375 2.440 nonbonded pdb=" O SER A 481 " pdb=" OG SER A 485 " model vdw 2.379 2.440 nonbonded pdb=" OD1 ASP B 821 " pdb=" NZ LYS B 849 " model vdw 2.379 2.520 nonbonded pdb=" O ALA A 945 " pdb=" OG SER A 973 " model vdw 2.383 2.440 ... (remaining 169833 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: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 24.230 Check model and map are aligned: 0.320 Set scattering table: 0.160 Process input model: 59.670 Find NCS groups from input model: 1.150 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.079 22011 Z= 0.730 Angle : 1.161 10.099 29697 Z= 0.806 Chirality : 0.070 0.330 3420 Planarity : 0.004 0.031 3765 Dihedral : 10.693 87.956 8187 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.74 % Allowed : 5.30 % Favored : 93.96 % Rotamer: Outliers : 0.17 % Allowed : 0.78 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 6.06 % 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: -0.39 (0.16), residues: 2700 helix: -0.10 (0.14), residues: 1140 sheet: 0.28 (0.29), residues: 351 loop : -0.43 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP C 917 HIS 0.004 0.001 HIS C 364 PHE 0.024 0.003 PHE B 253 TYR 0.029 0.004 TYR B 449 ARG 0.003 0.000 ARG A 285 *********************** 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 597 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 593 time to evaluate : 2.569 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 353 GLU cc_start: 0.8113 (tp30) cc_final: 0.7815 (pt0) REVERT: A 798 LEU cc_start: 0.8239 (tp) cc_final: 0.6928 (tp) REVERT: A 810 TYR cc_start: 0.7462 (m-80) cc_final: 0.7161 (m-80) REVERT: A 907 PRO cc_start: 0.7989 (Cg_exo) cc_final: 0.7669 (Cg_endo) REVERT: B 111 THR cc_start: 0.9363 (m) cc_final: 0.9040 (p) REVERT: B 691 ARG cc_start: 0.6901 (mtt180) cc_final: 0.6655 (mtt-85) REVERT: B 903 LEU cc_start: 0.7928 (mt) cc_final: 0.7662 (tp) REVERT: B 963 ASN cc_start: 0.6677 (m-40) cc_final: 0.6103 (t0) REVERT: B 997 LEU cc_start: 0.8706 (tp) cc_final: 0.8489 (tp) REVERT: C 135 THR cc_start: 0.8432 (p) cc_final: 0.8162 (t) REVERT: C 477 MET cc_start: 0.7885 (mmt) cc_final: 0.7495 (mmt) REVERT: C 547 LYS cc_start: 0.7234 (mttt) cc_final: 0.7010 (mttp) REVERT: C 563 GLN cc_start: 0.8201 (tt0) cc_final: 0.7984 (tt0) REVERT: C 568 LYS cc_start: 0.7851 (mttt) cc_final: 0.7641 (mtmm) REVERT: C 611 PHE cc_start: 0.6233 (m-80) cc_final: 0.5758 (m-10) REVERT: C 875 MET cc_start: 0.5206 (mtt) cc_final: 0.4066 (ppp) REVERT: C 878 LEU cc_start: 0.8270 (tp) cc_final: 0.7772 (mp) REVERT: C 917 TRP cc_start: 0.4607 (p90) cc_final: 0.2432 (p90) REVERT: C 958 MET cc_start: 0.7362 (tpp) cc_final: 0.6816 (tmm) outliers start: 4 outliers final: 2 residues processed: 596 average time/residue: 0.3676 time to fit residues: 324.3454 Evaluate side-chains 278 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 276 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain C residue 361 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 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 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN A 241 GLN A 269 HIS A 348 GLN A 364 HIS A 858 ASN B 151 GLN B 348 GLN B 573 GLN B 800 HIS B 916 ASN B 989 GLN C 147 HIS ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS C 273 ASN C 348 GLN C 411 GLN C 587 ASN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 GLN C 943 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22011 Z= 0.256 Angle : 0.691 12.324 29697 Z= 0.366 Chirality : 0.042 0.166 3420 Planarity : 0.004 0.057 3765 Dihedral : 4.934 31.438 2873 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.44 % Favored : 94.33 % Rotamer: Outliers : 2.06 % Allowed : 8.87 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.17), residues: 2700 helix: 0.73 (0.15), residues: 1197 sheet: 0.51 (0.28), residues: 327 loop : -0.86 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 917 HIS 0.007 0.001 HIS C 797 PHE 0.025 0.002 PHE B 684 TYR 0.019 0.002 TYR B 594 ARG 0.007 0.001 ARG B 453 *********************** 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 365 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 315 time to evaluate : 2.392 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: A 353 GLU cc_start: 0.8233 (tp30) cc_final: 0.7873 (pt0) REVERT: A 850 LEU cc_start: 0.7232 (mt) cc_final: 0.6979 (mt) REVERT: A 985 ARG cc_start: 0.5254 (mmt180) cc_final: 0.4386 (mtt180) REVERT: B 111 THR cc_start: 0.9292 (m) cc_final: 0.8890 (p) REVERT: B 256 GLN cc_start: 0.8335 (pm20) cc_final: 0.7793 (pp30) REVERT: B 671 LYS cc_start: 0.7953 (pttt) cc_final: 0.7581 (pptt) REVERT: B 691 ARG cc_start: 0.6823 (mtt180) cc_final: 0.6553 (mtt-85) REVERT: B 792 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8285 (mtmt) REVERT: B 963 ASN cc_start: 0.6880 (m-40) cc_final: 0.6420 (t0) REVERT: C 238 LYS cc_start: 0.9228 (tmtt) cc_final: 0.8985 (tmmt) REVERT: C 477 MET cc_start: 0.8162 (mmt) cc_final: 0.7380 (mmt) REVERT: C 556 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7201 (mt-10) REVERT: C 574 GLU cc_start: 0.8371 (tp30) cc_final: 0.8060 (tp30) REVERT: C 799 THR cc_start: 0.7394 (m) cc_final: 0.7140 (p) REVERT: C 838 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7343 (ptpt) REVERT: C 878 LEU cc_start: 0.8222 (tp) cc_final: 0.7874 (mp) REVERT: C 902 HIS cc_start: 0.5586 (OUTLIER) cc_final: 0.4624 (t-170) REVERT: C 917 TRP cc_start: 0.4953 (p90) cc_final: 0.2655 (p90) REVERT: C 963 ASN cc_start: 0.7660 (m-40) cc_final: 0.6891 (t0) outliers start: 50 outliers final: 35 residues processed: 354 average time/residue: 0.3314 time to fit residues: 183.0803 Evaluate side-chains 256 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 947 ASN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 835 ASN Chi-restraints excluded: chain C residue 902 HIS Chi-restraints excluded: chain C residue 943 ASN Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 245 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN A 404 HIS A 601 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 GLN ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 155 ASN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 943 ASN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22011 Z= 0.327 Angle : 0.685 13.092 29697 Z= 0.359 Chirality : 0.043 0.179 3420 Planarity : 0.004 0.053 3765 Dihedral : 5.104 31.786 2873 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 2.43 % Allowed : 10.23 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % 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: -0.09 (0.17), residues: 2700 helix: 0.79 (0.15), residues: 1215 sheet: 0.46 (0.29), residues: 309 loop : -1.08 (0.20), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 917 HIS 0.024 0.001 HIS A 269 PHE 0.022 0.002 PHE C 442 TYR 0.030 0.002 TYR C 679 ARG 0.007 0.001 ARG A 242 *********************** 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 308 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 249 time to evaluate : 2.583 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: A 353 GLU cc_start: 0.8235 (tp30) cc_final: 0.8033 (pt0) REVERT: A 477 MET cc_start: 0.8117 (mmm) cc_final: 0.7505 (mtt) REVERT: A 850 LEU cc_start: 0.7041 (mt) cc_final: 0.6636 (mt) REVERT: A 985 ARG cc_start: 0.5483 (mmt180) cc_final: 0.4481 (mtt180) REVERT: B 111 THR cc_start: 0.9362 (m) cc_final: 0.9011 (p) REVERT: B 256 GLN cc_start: 0.8455 (pm20) cc_final: 0.8111 (pp30) REVERT: B 274 MET cc_start: 0.8439 (mtp) cc_final: 0.8221 (mtm) REVERT: B 477 MET cc_start: 0.8095 (mmm) cc_final: 0.7352 (mmp) REVERT: B 594 TYR cc_start: 0.7922 (p90) cc_final: 0.7479 (p90) REVERT: B 671 LYS cc_start: 0.7967 (pttt) cc_final: 0.7585 (pptt) REVERT: B 792 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8362 (mtmm) REVERT: B 963 ASN cc_start: 0.7000 (m-40) cc_final: 0.6634 (t0) REVERT: C 477 MET cc_start: 0.8177 (mmt) cc_final: 0.7437 (mmt) REVERT: C 556 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7288 (mt-10) REVERT: C 682 LYS cc_start: 0.7686 (mttt) cc_final: 0.7254 (mmmt) REVERT: C 767 LYS cc_start: 0.7959 (tttt) cc_final: 0.7551 (mptt) REVERT: C 775 MET cc_start: 0.6458 (mtt) cc_final: 0.5754 (ttm) REVERT: C 799 THR cc_start: 0.7455 (m) cc_final: 0.7154 (p) REVERT: C 810 TYR cc_start: 0.7198 (m-80) cc_final: 0.6977 (m-80) REVERT: C 826 GLN cc_start: 0.7529 (mp10) cc_final: 0.7037 (mp10) REVERT: C 878 LEU cc_start: 0.8300 (tp) cc_final: 0.7902 (mp) REVERT: C 885 MET cc_start: 0.8434 (mmm) cc_final: 0.8233 (mtt) REVERT: C 902 HIS cc_start: 0.5687 (OUTLIER) cc_final: 0.4480 (t-170) REVERT: C 917 TRP cc_start: 0.5206 (p90) cc_final: 0.3071 (p90) REVERT: C 943 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6556 (m-40) REVERT: C 963 ASN cc_start: 0.7260 (m-40) cc_final: 0.6846 (t0) outliers start: 59 outliers final: 40 residues processed: 291 average time/residue: 0.2999 time to fit residues: 138.8757 Evaluate side-chains 248 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 206 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 693 GLN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 947 ASN Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 902 HIS Chi-restraints excluded: chain C residue 943 ASN Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 246 optimal weight: 8.9990 chunk 260 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN A 601 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22011 Z= 0.190 Angle : 0.593 13.410 29697 Z= 0.308 Chirality : 0.040 0.154 3420 Planarity : 0.004 0.048 3765 Dihedral : 4.875 33.095 2873 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.19 % Favored : 93.78 % Rotamer: Outliers : 2.27 % Allowed : 11.59 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 3.03 % 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: -0.04 (0.17), residues: 2700 helix: 1.01 (0.16), residues: 1212 sheet: 0.09 (0.29), residues: 327 loop : -1.15 (0.20), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 917 HIS 0.004 0.001 HIS B 797 PHE 0.022 0.001 PHE B 684 TYR 0.018 0.001 TYR C 679 ARG 0.005 0.000 ARG C 240 *********************** 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 289 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 234 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8248 (tp30) cc_final: 0.8048 (pt0) REVERT: A 477 MET cc_start: 0.8088 (mmm) cc_final: 0.7780 (mtt) REVERT: A 985 ARG cc_start: 0.5545 (mmt180) cc_final: 0.4479 (mtt180) REVERT: B 111 THR cc_start: 0.9342 (m) cc_final: 0.8978 (p) REVERT: B 256 GLN cc_start: 0.8460 (pm20) cc_final: 0.8223 (pp30) REVERT: B 274 MET cc_start: 0.8305 (mtp) cc_final: 0.8098 (mtm) REVERT: B 388 ARG cc_start: 0.8771 (ttm110) cc_final: 0.8527 (ttm110) REVERT: B 477 MET cc_start: 0.8055 (mmm) cc_final: 0.7767 (mmt) REVERT: B 594 TYR cc_start: 0.7849 (p90) cc_final: 0.7346 (p90) REVERT: B 671 LYS cc_start: 0.7997 (pttt) cc_final: 0.7625 (pptt) REVERT: B 958 MET cc_start: 0.8577 (mmp) cc_final: 0.8257 (mmm) REVERT: B 963 ASN cc_start: 0.7019 (m-40) cc_final: 0.6659 (t0) REVERT: C 477 MET cc_start: 0.8227 (mmt) cc_final: 0.7364 (mmt) REVERT: C 556 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7277 (mt-10) REVERT: C 562 TYR cc_start: 0.8701 (t80) cc_final: 0.8122 (t80) REVERT: C 767 LYS cc_start: 0.7980 (tttt) cc_final: 0.7508 (mmtt) REVERT: C 799 THR cc_start: 0.7451 (m) cc_final: 0.7170 (p) REVERT: C 878 LEU cc_start: 0.8242 (tp) cc_final: 0.7958 (mp) REVERT: C 917 TRP cc_start: 0.4706 (p90) cc_final: 0.2584 (p90) REVERT: C 963 ASN cc_start: 0.6966 (m-40) cc_final: 0.6730 (t0) REVERT: C 983 LEU cc_start: 0.8425 (mm) cc_final: 0.8191 (tp) outliers start: 55 outliers final: 31 residues processed: 278 average time/residue: 0.3211 time to fit residues: 143.2939 Evaluate side-chains 242 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 211 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 947 ASN Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 222 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN A 411 GLN A 601 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 GLN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 GLN ** C 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22011 Z= 0.199 Angle : 0.585 13.991 29697 Z= 0.303 Chirality : 0.040 0.171 3420 Planarity : 0.004 0.046 3765 Dihedral : 4.755 30.671 2872 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.41 % Favored : 93.56 % Rotamer: Outliers : 2.43 % Allowed : 12.13 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % 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: -0.02 (0.17), residues: 2700 helix: 1.06 (0.16), residues: 1230 sheet: 0.28 (0.30), residues: 303 loop : -1.27 (0.20), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1005 HIS 0.004 0.001 HIS C 731 PHE 0.021 0.001 PHE A 684 TYR 0.018 0.001 TYR B 715 ARG 0.014 0.000 ARG B 691 *********************** 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 292 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 233 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7529 (pp30) REVERT: A 353 GLU cc_start: 0.8244 (tp30) cc_final: 0.8043 (pt0) REVERT: A 985 ARG cc_start: 0.5420 (mmt180) cc_final: 0.4431 (mtt180) REVERT: B 111 THR cc_start: 0.9381 (m) cc_final: 0.9059 (p) REVERT: B 274 MET cc_start: 0.8285 (mtp) cc_final: 0.8019 (mtm) REVERT: B 388 ARG cc_start: 0.8785 (ttm110) cc_final: 0.8536 (ttm110) REVERT: B 477 MET cc_start: 0.8099 (mmm) cc_final: 0.7806 (mmt) REVERT: B 671 LYS cc_start: 0.8033 (pttt) cc_final: 0.7644 (pptt) REVERT: B 793 MET cc_start: 0.7617 (tpp) cc_final: 0.6865 (ttt) REVERT: B 958 MET cc_start: 0.8572 (mmp) cc_final: 0.8336 (mmm) REVERT: B 963 ASN cc_start: 0.6980 (m-40) cc_final: 0.6517 (t0) REVERT: C 411 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8510 (pp30) REVERT: C 477 MET cc_start: 0.8266 (mmt) cc_final: 0.7387 (mmt) REVERT: C 556 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7348 (mt-10) REVERT: C 562 TYR cc_start: 0.8734 (t80) cc_final: 0.8191 (t80) REVERT: C 767 LYS cc_start: 0.7983 (tttt) cc_final: 0.7608 (mmtt) REVERT: C 799 THR cc_start: 0.7386 (m) cc_final: 0.7099 (p) REVERT: C 878 LEU cc_start: 0.8274 (tp) cc_final: 0.8032 (mp) REVERT: C 917 TRP cc_start: 0.4723 (p90) cc_final: 0.2624 (p90) REVERT: C 963 ASN cc_start: 0.6884 (m-40) cc_final: 0.6683 (t0) outliers start: 59 outliers final: 41 residues processed: 276 average time/residue: 0.3082 time to fit residues: 137.8449 Evaluate side-chains 252 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 210 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 947 ASN Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 931 PHE Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 153 optimal weight: 0.0070 chunk 64 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 601 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 ASN ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 GLN C 693 GLN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 865 ASN ** C 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22011 Z= 0.165 Angle : 0.578 13.884 29697 Z= 0.295 Chirality : 0.039 0.206 3420 Planarity : 0.003 0.043 3765 Dihedral : 4.624 31.686 2871 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.30 % Favored : 93.67 % Rotamer: Outliers : 2.43 % Allowed : 13.00 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % 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: -0.08 (0.17), residues: 2700 helix: 1.10 (0.16), residues: 1233 sheet: 0.01 (0.29), residues: 309 loop : -1.35 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C1005 HIS 0.004 0.001 HIS C 731 PHE 0.029 0.001 PHE B 684 TYR 0.022 0.001 TYR B 594 ARG 0.007 0.000 ARG B 691 *********************** 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 298 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 239 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7573 (pp30) REVERT: A 353 GLU cc_start: 0.8225 (tp30) cc_final: 0.8019 (pt0) REVERT: A 985 ARG cc_start: 0.5361 (mmt180) cc_final: 0.4424 (mtt180) REVERT: B 111 THR cc_start: 0.9341 (m) cc_final: 0.9033 (p) REVERT: B 388 ARG cc_start: 0.8770 (ttm110) cc_final: 0.8500 (ttm110) REVERT: B 477 MET cc_start: 0.8095 (mmm) cc_final: 0.7768 (mmt) REVERT: B 671 LYS cc_start: 0.8018 (pttt) cc_final: 0.7630 (pptt) REVERT: B 862 LYS cc_start: 0.6817 (mmtt) cc_final: 0.6498 (mmmt) REVERT: B 963 ASN cc_start: 0.6834 (m-40) cc_final: 0.6455 (t0) REVERT: C 477 MET cc_start: 0.8268 (mmt) cc_final: 0.7387 (mmt) REVERT: C 556 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7322 (mt-10) REVERT: C 767 LYS cc_start: 0.7943 (tttt) cc_final: 0.7564 (mptt) REVERT: C 824 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7390 (mm-30) REVERT: C 878 LEU cc_start: 0.8236 (tp) cc_final: 0.7971 (mp) REVERT: C 902 HIS cc_start: 0.5264 (OUTLIER) cc_final: 0.4312 (t-170) REVERT: C 917 TRP cc_start: 0.4761 (p90) cc_final: 0.2731 (p90) REVERT: C 1005 TRP cc_start: 0.8309 (m-10) cc_final: 0.8081 (m-10) outliers start: 59 outliers final: 41 residues processed: 285 average time/residue: 0.2991 time to fit residues: 136.2438 Evaluate side-chains 254 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 211 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 947 ASN Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 549 ILE Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 902 HIS Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 997 LEU Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 148 optimal weight: 20.0000 chunk 190 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 219 optimal weight: 0.5980 chunk 145 optimal weight: 0.2980 chunk 260 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 601 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 GLN ** C 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22011 Z= 0.196 Angle : 0.596 13.867 29697 Z= 0.304 Chirality : 0.040 0.242 3420 Planarity : 0.003 0.044 3765 Dihedral : 4.595 29.657 2871 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.52 % Favored : 93.41 % Rotamer: Outliers : 2.48 % Allowed : 13.66 % Favored : 83.87 % 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: -0.13 (0.17), residues: 2700 helix: 1.13 (0.16), residues: 1233 sheet: -0.26 (0.28), residues: 333 loop : -1.41 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C1005 HIS 0.005 0.001 HIS C 731 PHE 0.029 0.001 PHE A 684 TYR 0.013 0.001 TYR A 594 ARG 0.004 0.000 ARG B 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 278 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 218 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7710 (pp30) REVERT: B 111 THR cc_start: 0.9393 (m) cc_final: 0.9104 (p) REVERT: B 274 MET cc_start: 0.8213 (mtp) cc_final: 0.7954 (mtm) REVERT: B 388 ARG cc_start: 0.8781 (ttm110) cc_final: 0.8500 (ttm110) REVERT: B 477 MET cc_start: 0.8097 (mmm) cc_final: 0.7771 (mmt) REVERT: B 963 ASN cc_start: 0.6892 (m-40) cc_final: 0.6471 (t0) REVERT: C 477 MET cc_start: 0.8301 (mmt) cc_final: 0.7411 (mmt) REVERT: C 556 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7358 (mt-10) REVERT: C 562 TYR cc_start: 0.8701 (t80) cc_final: 0.8137 (t80) REVERT: C 767 LYS cc_start: 0.7951 (tttt) cc_final: 0.7605 (mmtt) REVERT: C 878 LEU cc_start: 0.8261 (tp) cc_final: 0.8055 (mp) REVERT: C 917 TRP cc_start: 0.4938 (p90) cc_final: 0.2931 (p90) outliers start: 60 outliers final: 49 residues processed: 262 average time/residue: 0.3039 time to fit residues: 127.6500 Evaluate side-chains 253 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 947 ASN Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 931 PHE Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 10.0000 chunk 103 optimal weight: 0.3980 chunk 155 optimal weight: 0.3980 chunk 78 optimal weight: 0.0020 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 177 optimal weight: 0.0980 chunk 128 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS A 657 GLN A 963 ASN B 357 HIS B 989 GLN C 151 GLN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22011 Z= 0.141 Angle : 0.589 14.790 29697 Z= 0.296 Chirality : 0.039 0.245 3420 Planarity : 0.003 0.041 3765 Dihedral : 4.490 31.468 2871 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 1.90 % Allowed : 14.60 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % 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: 1.32 (0.16), residues: 1209 sheet: -0.52 (0.27), residues: 369 loop : -1.19 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C1005 HIS 0.004 0.001 HIS C 731 PHE 0.027 0.001 PHE B 684 TYR 0.014 0.001 TYR B 594 ARG 0.004 0.000 ARG B 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 266 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 220 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LYS cc_start: 0.8832 (tppt) cc_final: 0.7661 (mtmm) REVERT: A 241 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7766 (pp30) REVERT: A 850 LEU cc_start: 0.7879 (pp) cc_final: 0.7183 (mt) REVERT: A 862 LYS cc_start: 0.4606 (tptp) cc_final: 0.4347 (mmtt) REVERT: A 998 GLN cc_start: 0.7304 (mp10) cc_final: 0.7092 (mp10) REVERT: B 111 THR cc_start: 0.9318 (m) cc_final: 0.9046 (p) REVERT: B 388 ARG cc_start: 0.8771 (ttm110) cc_final: 0.8485 (ttm110) REVERT: B 477 MET cc_start: 0.8063 (mmm) cc_final: 0.7728 (mmt) REVERT: B 963 ASN cc_start: 0.6818 (m-40) cc_final: 0.6438 (t0) REVERT: C 477 MET cc_start: 0.8258 (mmt) cc_final: 0.7354 (mmt) REVERT: C 556 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7321 (mt-10) REVERT: C 562 TYR cc_start: 0.8652 (t80) cc_final: 0.8147 (t80) REVERT: C 661 THR cc_start: 0.7611 (p) cc_final: 0.7207 (p) REVERT: C 767 LYS cc_start: 0.7882 (tttt) cc_final: 0.7559 (mptt) REVERT: C 878 LEU cc_start: 0.8326 (tp) cc_final: 0.8075 (mp) REVERT: C 917 TRP cc_start: 0.4624 (p90) cc_final: 0.2602 (p90) outliers start: 46 outliers final: 37 residues processed: 255 average time/residue: 0.3015 time to fit residues: 124.5707 Evaluate side-chains 250 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 212 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 947 ASN Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 931 PHE Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 219 optimal weight: 0.7980 chunk 229 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 ASN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22011 Z= 0.186 Angle : 0.605 15.045 29697 Z= 0.304 Chirality : 0.040 0.239 3420 Planarity : 0.003 0.043 3765 Dihedral : 4.490 28.883 2871 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.63 % Favored : 93.30 % Rotamer: Outliers : 2.10 % Allowed : 14.36 % Favored : 83.54 % 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: 0.05 (0.17), residues: 2700 helix: 1.35 (0.16), residues: 1209 sheet: -0.46 (0.28), residues: 366 loop : -1.25 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C1005 HIS 0.007 0.001 HIS C 731 PHE 0.037 0.001 PHE A 684 TYR 0.013 0.001 TYR A 594 ARG 0.007 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 269 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 218 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7779 (pp30) REVERT: A 862 LYS cc_start: 0.4731 (tptp) cc_final: 0.4368 (mmtt) REVERT: A 998 GLN cc_start: 0.7393 (mp10) cc_final: 0.7155 (mp10) REVERT: B 111 THR cc_start: 0.9391 (m) cc_final: 0.9137 (p) REVERT: B 388 ARG cc_start: 0.8772 (ttm110) cc_final: 0.8480 (ttm110) REVERT: B 477 MET cc_start: 0.8053 (mmm) cc_final: 0.7717 (mmt) REVERT: B 793 MET cc_start: 0.7861 (tpp) cc_final: 0.7650 (ttt) REVERT: C 477 MET cc_start: 0.8271 (mmt) cc_final: 0.7380 (mmt) REVERT: C 556 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7364 (mt-10) REVERT: C 562 TYR cc_start: 0.8661 (t80) cc_final: 0.8122 (t80) REVERT: C 767 LYS cc_start: 0.7918 (tttt) cc_final: 0.7609 (mptt) REVERT: C 878 LEU cc_start: 0.8399 (tp) cc_final: 0.7904 (mt) REVERT: C 881 LEU cc_start: 0.8436 (tp) cc_final: 0.7701 (pp) REVERT: C 917 TRP cc_start: 0.4873 (p90) cc_final: 0.2955 (p90) outliers start: 51 outliers final: 43 residues processed: 254 average time/residue: 0.2973 time to fit residues: 121.9757 Evaluate side-chains 252 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 208 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 947 ASN Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 931 PHE Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 6.9990 chunk 256 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 121 optimal weight: 0.0050 chunk 178 optimal weight: 9.9990 chunk 268 optimal weight: 0.9980 chunk 247 optimal weight: 8.9990 chunk 214 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 ASN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 963 ASN C 433 GLN ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22011 Z= 0.258 Angle : 0.651 15.259 29697 Z= 0.327 Chirality : 0.041 0.231 3420 Planarity : 0.004 0.042 3765 Dihedral : 4.641 30.702 2871 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.96 % Favored : 93.00 % Rotamer: Outliers : 1.94 % Allowed : 14.89 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % 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: 1.08 (0.16), residues: 1248 sheet: -0.52 (0.28), residues: 366 loop : -1.42 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C1005 HIS 0.007 0.001 HIS C 731 PHE 0.041 0.002 PHE B 931 TYR 0.013 0.001 TYR B 594 ARG 0.006 0.000 ARG C 925 ********************** 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 257 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 210 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7801 (pp30) REVERT: A 888 TRP cc_start: 0.4961 (t60) cc_final: 0.4697 (t60) REVERT: A 965 LYS cc_start: 0.6372 (mmpt) cc_final: 0.6169 (mmpt) REVERT: B 111 THR cc_start: 0.9408 (m) cc_final: 0.9142 (p) REVERT: B 388 ARG cc_start: 0.8767 (ttm110) cc_final: 0.8473 (ttm110) REVERT: B 477 MET cc_start: 0.8008 (mmm) cc_final: 0.7663 (mmt) REVERT: B 611 PHE cc_start: 0.8406 (m-80) cc_final: 0.8059 (t80) REVERT: C 477 MET cc_start: 0.8319 (mmt) cc_final: 0.7408 (mmt) REVERT: C 556 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7423 (mt-10) REVERT: C 562 TYR cc_start: 0.8686 (t80) cc_final: 0.8178 (t80) REVERT: C 767 LYS cc_start: 0.7949 (tttt) cc_final: 0.7615 (mmtt) REVERT: C 878 LEU cc_start: 0.8422 (tp) cc_final: 0.7923 (mt) REVERT: C 881 LEU cc_start: 0.8399 (tp) cc_final: 0.7690 (pp) REVERT: C 917 TRP cc_start: 0.4993 (p90) cc_final: 0.3030 (p90) outliers start: 47 outliers final: 41 residues processed: 244 average time/residue: 0.2972 time to fit residues: 117.6603 Evaluate side-chains 243 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 201 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 947 ASN Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 957 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 931 PHE Chi-restraints excluded: chain C residue 1015 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 3.9990 chunk 228 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 214 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 601 HIS ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS ** C 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 HIS ** C 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.164171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.132637 restraints weight = 39487.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.128014 restraints weight = 60754.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125983 restraints weight = 50892.457| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22011 Z= 0.192 Angle : 0.620 15.220 29697 Z= 0.310 Chirality : 0.041 0.234 3420 Planarity : 0.003 0.044 3765 Dihedral : 4.568 30.969 2871 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.63 % Favored : 93.33 % Rotamer: Outliers : 2.10 % Allowed : 14.73 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 1.52 % 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: -0.17 (0.17), residues: 2700 helix: 1.15 (0.16), residues: 1245 sheet: -0.61 (0.28), residues: 369 loop : -1.42 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C1005 HIS 0.007 0.001 HIS C 731 PHE 0.017 0.001 PHE C 442 TYR 0.013 0.001 TYR A 594 ARG 0.006 0.000 ARG C 925 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4192.01 seconds wall clock time: 77 minutes 9.41 seconds (4629.41 seconds total)