Starting phenix.real_space_refine on Wed Aug 7 15:10:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy9_37920/08_2024/8wy9_37920.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy9_37920/08_2024/8wy9_37920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy9_37920/08_2024/8wy9_37920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy9_37920/08_2024/8wy9_37920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy9_37920/08_2024/8wy9_37920.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy9_37920/08_2024/8wy9_37920.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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 75 5.16 5 C 13028 2.51 5 N 3257 2.21 5 O 3769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A ASP 553": "OD1" <-> "OD2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A ASP 581": "OD1" <-> "OD2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 759": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 590": "OD1" <-> "OD2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "B PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 682": "OE1" <-> "OE2" Residue "B TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C ASP 173": "OD1" <-> "OD2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D GLU 284": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20129 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7786 Classifications: {'peptide': 932} Link IDs: {'PTRANS': 19, 'TRANS': 912} Chain breaks: 7 Chain: "B" Number of atoms: 7869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7869 Classifications: {'peptide': 940} Link IDs: {'PTRANS': 19, 'TRANS': 920} Chain breaks: 7 Chain: "C" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2225 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain: "D" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2249 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 10, 'TRANS': 264} Time building chain proxies: 12.95, per 1000 atoms: 0.64 Number of scatterers: 20129 At special positions: 0 Unit cell: (100.067, 126.531, 180.286, 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 75 16.00 O 3769 8.00 N 3257 7.00 C 13028 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: 7.53 Conformation dependent library (CDL) restraints added in 3.7 seconds 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4614 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 7 sheets defined 70.6% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 Processing helix chain 'A' and resid 47 through 53 removed outlier: 4.031A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.707A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.597A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.745A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.522A pdb=" N ASN A 182 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 183 " --> pdb=" O GLY A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 183' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.793A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.553A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 372 removed outlier: 4.035A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 469 through 494 Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.773A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 572 Processing helix chain 'A' and resid 579 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.856A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.837A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 750 through 765 removed outlier: 4.288A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 810 Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.521A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 841 removed outlier: 3.724A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 857 removed outlier: 3.905A pdb=" N HIS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 853 " --> pdb=" O ALA A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 897 removed outlier: 3.670A pdb=" N ILE A 897 " --> pdb=" O LYS A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 922 removed outlier: 4.020A pdb=" N PHE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 917 " --> pdb=" O MET A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 removed outlier: 4.058A pdb=" N GLU A 931 " --> pdb=" O SER A 928 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 removed outlier: 3.866A pdb=" N LYS A 953 " --> pdb=" O ASP A 950 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 954 " --> pdb=" O TYR A 951 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 950 through 954' Processing helix chain 'A' and resid 955 through 956 No H-bonds generated for 'chain 'A' and resid 955 through 956' Processing helix chain 'A' and resid 957 through 962 removed outlier: 3.955A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 962 " --> pdb=" O TRP A 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 962' Processing helix chain 'A' and resid 963 through 974 removed outlier: 4.321A pdb=" N LYS A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 991 Processing helix chain 'A' and resid 994 through 1004 Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.947A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.784A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 removed outlier: 3.569A pdb=" N TYR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.592A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.901A pdb=" N VAL B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 160' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 234 removed outlier: 3.566A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'B' and resid 281 through 298 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 326 through 334 removed outlier: 3.604A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.579A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 493 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.420A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 559 through 563 removed outlier: 3.634A pdb=" N ASN B 563 " --> pdb=" O GLU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 598 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 635 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 700 Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.862A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 812 removed outlier: 4.040A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 Processing helix chain 'B' and resid 831 through 839 removed outlier: 3.599A pdb=" N ILE B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 846 through 856 removed outlier: 3.530A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 872 Processing helix chain 'B' and resid 878 through 895 Processing helix chain 'B' and resid 912 through 922 Processing helix chain 'B' and resid 929 through 934 removed outlier: 3.564A pdb=" N GLU B 932 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 removed outlier: 3.535A pdb=" N ASP B 941 " --> pdb=" O ASP B 937 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP B 945 " --> pdb=" O ASP B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 955 through 956 No H-bonds generated for 'chain 'B' and resid 955 through 956' Processing helix chain 'B' and resid 957 through 962 removed outlier: 4.054A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 976 through 991 Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.930A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.791A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 72 Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.706A pdb=" N LEU C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.769A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.596A pdb=" N VAL C 183 " --> pdb=" O GLY C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 222 through 235 removed outlier: 3.707A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 264 removed outlier: 3.525A pdb=" N TYR C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 297 removed outlier: 3.851A pdb=" N ARG C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 39 removed outlier: 3.936A pdb=" N GLU D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 54 removed outlier: 3.993A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.769A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.898A pdb=" N LEU D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.873A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 254 through 263 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 296 removed outlier: 4.065A pdb=" N ARG D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.332A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.808A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'B' and resid 646 through 647 Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.045A pdb=" N SER C 150 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS C 169 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 152 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE C 213 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE C 246 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE C 215 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.125A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS D 128 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3171 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: 7.27 Time building geometry restraints manager: 8.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6376 1.34 - 1.46: 5165 1.46 - 1.58: 8927 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 20594 Sorted by residual: bond pdb=" CB PRO B 506 " pdb=" CG PRO B 506 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.70e+00 bond pdb=" CB GLU A 510 " pdb=" CG GLU A 510 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" CG PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 1.503 1.463 0.040 3.40e-02 8.65e+02 1.36e+00 bond pdb=" CB PRO A 74 " pdb=" CG PRO A 74 " ideal model delta sigma weight residual 1.492 1.547 -0.055 5.00e-02 4.00e+02 1.21e+00 bond pdb=" CB ASN B 797 " pdb=" CG ASN B 797 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.14e+00 ... (remaining 20589 not shown) Histogram of bond angle deviations from ideal: 97.14 - 104.52: 184 104.52 - 111.91: 9401 111.91 - 119.29: 7164 119.29 - 126.68: 10810 126.68 - 134.07: 206 Bond angle restraints: 27765 Sorted by residual: angle pdb=" N PRO A 74 " pdb=" CD PRO A 74 " pdb=" CG PRO A 74 " ideal model delta sigma weight residual 103.20 97.54 5.66 1.50e+00 4.44e-01 1.43e+01 angle pdb=" CA PRO A 74 " pdb=" N PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 112.00 107.00 5.00 1.40e+00 5.10e-01 1.27e+01 angle pdb=" CA LEU B 838 " pdb=" CB LEU B 838 " pdb=" CG LEU B 838 " ideal model delta sigma weight residual 116.30 127.45 -11.15 3.50e+00 8.16e-02 1.02e+01 angle pdb=" CB GLU A 510 " pdb=" CG GLU A 510 " pdb=" CD GLU A 510 " ideal model delta sigma weight residual 112.60 117.57 -4.97 1.70e+00 3.46e-01 8.55e+00 angle pdb=" CA GLU A 510 " pdb=" CB GLU A 510 " pdb=" CG GLU A 510 " ideal model delta sigma weight residual 114.10 119.85 -5.75 2.00e+00 2.50e-01 8.26e+00 ... (remaining 27760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 10325 17.83 - 35.66: 1445 35.66 - 53.49: 399 53.49 - 71.31: 79 71.31 - 89.14: 21 Dihedral angle restraints: 12269 sinusoidal: 5093 harmonic: 7176 Sorted by residual: dihedral pdb=" CA GLU A 923 " pdb=" C GLU A 923 " pdb=" N GLU A 924 " pdb=" CA GLU A 924 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA TYR D 166 " pdb=" C TYR D 166 " pdb=" N LEU D 167 " pdb=" CA LEU D 167 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR A 166 " pdb=" C TYR A 166 " pdb=" N LEU A 167 " pdb=" CA LEU A 167 " ideal model delta harmonic sigma weight residual 180.00 161.31 18.69 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 12266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2451 0.049 - 0.099: 437 0.099 - 0.148: 67 0.148 - 0.197: 0 0.197 - 0.246: 2 Chirality restraints: 2957 Sorted by residual: chirality pdb=" CG LEU A 966 " pdb=" CB LEU A 966 " pdb=" CD1 LEU A 966 " pdb=" CD2 LEU A 966 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CG LEU B 363 " pdb=" CB LEU B 363 " pdb=" CD1 LEU B 363 " pdb=" CD2 LEU B 363 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CG LEU D 228 " pdb=" CB LEU D 228 " pdb=" CD1 LEU D 228 " pdb=" CD2 LEU D 228 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 2954 not shown) Planarity restraints: 3536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 73 " -0.041 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO A 74 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 744 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.71e+00 pdb=" N PRO B 745 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 745 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 745 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 510 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" CD GLU A 510 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A 510 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 510 " 0.011 2.00e-02 2.50e+03 ... (remaining 3533 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 307 2.65 - 3.21: 18648 3.21 - 3.77: 33334 3.77 - 4.34: 47436 4.34 - 4.90: 75015 Nonbonded interactions: 174740 Sorted by model distance: nonbonded pdb=" O VAL A 470 " pdb=" OG SER A 474 " model vdw 2.086 3.040 nonbonded pdb=" O TYR B 313 " pdb=" OG SER B 317 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR A 324 " pdb=" OD1 ASP A 590 " model vdw 2.185 3.040 nonbonded pdb=" O TYR C 197 " pdb=" OG SER C 201 " model vdw 2.187 3.040 nonbonded pdb=" OG SER A 37 " pdb=" O MET A 124 " model vdw 2.190 3.040 ... (remaining 174735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 399 or resid 406 through 493 or resid 504 throu \ gh 565 or resid 579 through 786 or resid 793 through 1005)) selection = (chain 'B' and (resid 22 through 462 or resid 468 through 629 or resid 645 throu \ gh 700 or resid 703 through 1005)) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 26 through 297) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.880 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 56.380 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 : 0.002 0.065 20594 Z= 0.149 Angle : 0.508 11.154 27765 Z= 0.268 Chirality : 0.038 0.246 2957 Planarity : 0.003 0.060 3536 Dihedral : 17.958 89.142 7655 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.47 % Allowed : 26.86 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2383 helix: 0.91 (0.13), residues: 1496 sheet: -0.82 (0.67), residues: 40 loop : -0.09 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 757 HIS 0.003 0.001 HIS B 978 PHE 0.016 0.001 PHE A 943 TYR 0.021 0.001 TYR A 709 ARG 0.008 0.001 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 227 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 989 LYS cc_start: 0.8244 (mptt) cc_final: 0.7871 (mptt) REVERT: B 776 ASP cc_start: 0.8208 (t70) cc_final: 0.7930 (t0) REVERT: B 913 MET cc_start: 0.7842 (ptm) cc_final: 0.7476 (pmm) REVERT: D 216 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8587 (pp) outliers start: 77 outliers final: 57 residues processed: 298 average time/residue: 1.2406 time to fit residues: 421.0651 Evaluate side-chains 253 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 195 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 553 ASP Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 73 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 391 ASN A 475 GLN A 711 GLN A 797 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN D 278 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20594 Z= 0.202 Angle : 0.525 9.949 27765 Z= 0.279 Chirality : 0.040 0.178 2957 Planarity : 0.004 0.054 3536 Dihedral : 6.623 63.648 2755 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.28 % Allowed : 25.06 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2383 helix: 1.15 (0.13), residues: 1506 sheet: -1.16 (0.64), residues: 32 loop : 0.03 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 757 HIS 0.004 0.001 HIS A 128 PHE 0.013 0.001 PHE A 856 TYR 0.012 0.001 TYR A 755 ARG 0.007 0.001 ARG B 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 223 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 ARG cc_start: 0.7982 (ttm170) cc_final: 0.7764 (ttt180) REVERT: A 989 LYS cc_start: 0.8328 (mptt) cc_final: 0.8060 (mmmm) REVERT: A 995 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8614 (tpm170) REVERT: B 491 GLN cc_start: 0.7351 (tm-30) cc_final: 0.7148 (tm-30) REVERT: B 776 ASP cc_start: 0.8245 (t70) cc_final: 0.8000 (t0) REVERT: B 913 MET cc_start: 0.7781 (ptm) cc_final: 0.7475 (pmm) outliers start: 95 outliers final: 31 residues processed: 299 average time/residue: 1.2101 time to fit residues: 414.5656 Evaluate side-chains 234 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 236 optimal weight: 0.5980 chunk 195 optimal weight: 0.9980 chunk 217 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 175 optimal weight: 20.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 475 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN D 278 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20594 Z= 0.243 Angle : 0.519 10.252 27765 Z= 0.273 Chirality : 0.040 0.157 2957 Planarity : 0.003 0.046 3536 Dihedral : 5.268 57.289 2684 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.37 % Allowed : 24.65 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2383 helix: 1.17 (0.13), residues: 1518 sheet: -1.49 (0.65), residues: 32 loop : -0.04 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 757 HIS 0.005 0.001 HIS A 128 PHE 0.014 0.001 PHE A 856 TYR 0.016 0.001 TYR A 804 ARG 0.008 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 220 time to evaluate : 2.524 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: A 531 MET cc_start: 0.8297 (mmt) cc_final: 0.8062 (mmm) REVERT: A 875 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7310 (p0) REVERT: A 915 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7989 (p) REVERT: A 976 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6494 (ptp) REVERT: A 989 LYS cc_start: 0.8407 (mptt) cc_final: 0.7904 (mptt) REVERT: A 995 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8593 (tpm170) REVERT: B 491 GLN cc_start: 0.7400 (tm-30) cc_final: 0.7175 (tm-30) REVERT: B 557 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8434 (tmmm) REVERT: B 776 ASP cc_start: 0.8256 (t70) cc_final: 0.8009 (t0) REVERT: B 913 MET cc_start: 0.7815 (ptm) cc_final: 0.7556 (pmm) REVERT: B 936 MET cc_start: 0.3646 (OUTLIER) cc_final: 0.3226 (mpp) REVERT: D 105 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8523 (ttpt) REVERT: D 147 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7154 (ptpt) REVERT: D 181 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: D 233 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7502 (ptp90) outliers start: 97 outliers final: 33 residues processed: 294 average time/residue: 1.2031 time to fit residues: 404.0911 Evaluate side-chains 244 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 201 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 875 ASP Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 979 HIS Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 147 optimal weight: 0.4980 chunk 220 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 208 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 475 GLN A 523 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN D 278 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20594 Z= 0.179 Angle : 0.493 10.395 27765 Z= 0.258 Chirality : 0.039 0.146 2957 Planarity : 0.003 0.044 3536 Dihedral : 5.048 59.043 2677 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.42 % Allowed : 24.06 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2383 helix: 1.25 (0.13), residues: 1528 sheet: -1.76 (0.64), residues: 32 loop : -0.02 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 958 HIS 0.006 0.001 HIS A 979 PHE 0.013 0.001 PHE A 856 TYR 0.016 0.001 TYR A 951 ARG 0.009 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 217 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8331 (tp) REVERT: A 915 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7980 (p) REVERT: A 976 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6618 (ptt) REVERT: A 989 LYS cc_start: 0.8457 (mptt) cc_final: 0.7924 (mptt) REVERT: A 995 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8616 (tpm170) REVERT: B 776 ASP cc_start: 0.8251 (t70) cc_final: 0.8015 (t0) REVERT: B 913 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7576 (pmm) REVERT: B 936 MET cc_start: 0.3555 (OUTLIER) cc_final: 0.3085 (mpp) REVERT: C 145 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6990 (mpp80) REVERT: D 147 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7159 (ptpt) REVERT: D 181 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: D 233 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7512 (ptp90) outliers start: 98 outliers final: 38 residues processed: 289 average time/residue: 1.2500 time to fit residues: 413.7555 Evaluate side-chains 249 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 201 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 475 GLN A 829 GLN A 832 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN D 202 ASN D 278 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20594 Z= 0.254 Angle : 0.515 10.653 27765 Z= 0.270 Chirality : 0.040 0.148 2957 Planarity : 0.003 0.045 3536 Dihedral : 4.931 59.630 2673 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.55 % Allowed : 24.02 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2383 helix: 1.23 (0.13), residues: 1527 sheet: -1.72 (0.64), residues: 32 loop : -0.04 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 958 HIS 0.014 0.001 HIS A 979 PHE 0.014 0.001 PHE A 856 TYR 0.019 0.001 TYR A 755 ARG 0.010 0.001 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 214 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8318 (tp) REVERT: A 915 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7931 (p) REVERT: A 989 LYS cc_start: 0.8525 (mptt) cc_final: 0.7938 (mptt) REVERT: A 995 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8532 (tpm170) REVERT: A 999 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7899 (mt) REVERT: B 744 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8735 (t80) REVERT: B 776 ASP cc_start: 0.8296 (t70) cc_final: 0.8060 (t0) REVERT: B 913 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7578 (pmm) REVERT: B 936 MET cc_start: 0.3580 (OUTLIER) cc_final: 0.3076 (mpp) REVERT: B 1001 MET cc_start: 0.8565 (mtm) cc_final: 0.8232 (ttp) REVERT: D 147 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7243 (ptpt) REVERT: D 181 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: D 233 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7525 (ptp90) outliers start: 101 outliers final: 44 residues processed: 292 average time/residue: 1.2597 time to fit residues: 419.5088 Evaluate side-chains 251 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 197 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LYS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 233 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 475 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 236 GLN D 202 ASN D 278 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20594 Z= 0.291 Angle : 0.538 10.975 27765 Z= 0.280 Chirality : 0.041 0.164 2957 Planarity : 0.003 0.048 3536 Dihedral : 4.951 59.329 2672 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.82 % Allowed : 24.16 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2383 helix: 1.17 (0.13), residues: 1531 sheet: -1.78 (0.64), residues: 32 loop : -0.06 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 958 HIS 0.018 0.001 HIS A 979 PHE 0.015 0.001 PHE A 856 TYR 0.021 0.001 TYR A 709 ARG 0.011 0.001 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 212 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8324 (tp) REVERT: A 875 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7256 (p0) REVERT: A 915 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7918 (p) REVERT: A 939 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7442 (mm110) REVERT: A 989 LYS cc_start: 0.8588 (mptt) cc_final: 0.8040 (mptt) REVERT: A 995 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8476 (tpm170) REVERT: A 999 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7864 (mt) REVERT: B 744 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8750 (t80) REVERT: B 776 ASP cc_start: 0.8300 (t70) cc_final: 0.8066 (t0) REVERT: B 913 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7566 (pmm) REVERT: B 936 MET cc_start: 0.3574 (OUTLIER) cc_final: 0.3037 (mpp) REVERT: B 1001 MET cc_start: 0.8587 (mtm) cc_final: 0.8176 (ttp) REVERT: C 145 ARG cc_start: 0.7604 (tpp-160) cc_final: 0.6965 (mpp80) REVERT: D 147 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7367 (ptpt) REVERT: D 181 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8000 (pm20) REVERT: D 233 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7522 (ptp90) outliers start: 107 outliers final: 48 residues processed: 298 average time/residue: 1.2253 time to fit residues: 415.8963 Evaluate side-chains 259 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 199 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 727 LYS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 875 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 232 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 475 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN D 202 ASN D 278 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20594 Z= 0.194 Angle : 0.520 11.343 27765 Z= 0.270 Chirality : 0.040 0.187 2957 Planarity : 0.003 0.049 3536 Dihedral : 4.853 60.732 2672 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.06 % Allowed : 24.65 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.17), residues: 2383 helix: 1.27 (0.13), residues: 1535 sheet: -1.80 (0.60), residues: 44 loop : 0.02 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 958 HIS 0.014 0.001 HIS A 979 PHE 0.012 0.001 PHE B 699 TYR 0.022 0.001 TYR A 709 ARG 0.011 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 216 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8330 (tp) REVERT: A 839 PHE cc_start: 0.8365 (t80) cc_final: 0.8114 (t80) REVERT: A 939 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7444 (mm110) REVERT: A 976 MET cc_start: 0.6996 (ptp) cc_final: 0.6369 (ptp) REVERT: A 989 LYS cc_start: 0.8605 (mptt) cc_final: 0.8089 (mptt) REVERT: B 744 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8790 (t80) REVERT: B 776 ASP cc_start: 0.8284 (t70) cc_final: 0.8056 (t0) REVERT: B 913 MET cc_start: 0.7792 (ptm) cc_final: 0.7541 (pmm) REVERT: B 936 MET cc_start: 0.3585 (OUTLIER) cc_final: 0.2983 (mpp) REVERT: B 1001 MET cc_start: 0.8566 (mtm) cc_final: 0.8267 (ttp) REVERT: C 145 ARG cc_start: 0.7559 (tpp-160) cc_final: 0.6924 (mpp80) REVERT: D 181 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: D 233 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7523 (ptp90) outliers start: 90 outliers final: 45 residues processed: 288 average time/residue: 1.2413 time to fit residues: 408.6438 Evaluate side-chains 252 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 201 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 727 LYS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 21 optimal weight: 0.0030 chunk 182 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 475 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN D 202 ASN D 278 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20594 Z= 0.171 Angle : 0.519 11.257 27765 Z= 0.270 Chirality : 0.039 0.211 2957 Planarity : 0.003 0.054 3536 Dihedral : 4.792 61.727 2672 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.11 % Allowed : 25.96 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.17), residues: 2383 helix: 1.31 (0.13), residues: 1539 sheet: -1.78 (0.61), residues: 44 loop : 0.05 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 958 HIS 0.024 0.001 HIS A 979 PHE 0.011 0.001 PHE A 856 TYR 0.025 0.001 TYR A 951 ARG 0.013 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 212 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8334 (tp) REVERT: A 939 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7403 (mm110) REVERT: B 744 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8767 (t80) REVERT: B 776 ASP cc_start: 0.8281 (t70) cc_final: 0.8069 (t0) REVERT: B 913 MET cc_start: 0.7794 (ptm) cc_final: 0.7556 (pmm) REVERT: B 936 MET cc_start: 0.3450 (OUTLIER) cc_final: 0.2927 (mpp) REVERT: C 145 ARG cc_start: 0.7516 (tpp-160) cc_final: 0.6881 (mpp80) REVERT: D 233 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7471 (ptp90) REVERT: D 278 ASN cc_start: 0.7776 (t0) cc_final: 0.7462 (m110) outliers start: 69 outliers final: 36 residues processed: 267 average time/residue: 1.2413 time to fit residues: 377.6514 Evaluate side-chains 240 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 0.4980 chunk 203 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 169 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 195 optimal weight: 0.4980 chunk 204 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 475 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 236 GLN D 202 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20594 Z= 0.179 Angle : 0.531 12.104 27765 Z= 0.274 Chirality : 0.040 0.217 2957 Planarity : 0.003 0.042 3536 Dihedral : 4.676 61.591 2670 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.93 % Allowed : 26.23 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2383 helix: 1.33 (0.13), residues: 1538 sheet: -1.75 (0.61), residues: 44 loop : 0.03 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 958 HIS 0.021 0.001 HIS A 979 PHE 0.015 0.001 PHE A 839 TYR 0.017 0.001 TYR A 951 ARG 0.007 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 208 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8308 (tp) REVERT: A 939 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7412 (mm110) REVERT: B 744 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8747 (t80) REVERT: B 776 ASP cc_start: 0.8240 (t70) cc_final: 0.8005 (t0) REVERT: B 913 MET cc_start: 0.7799 (ptm) cc_final: 0.7555 (pmm) REVERT: B 936 MET cc_start: 0.3433 (OUTLIER) cc_final: 0.3065 (mpp) REVERT: D 233 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7474 (ptp90) REVERT: D 278 ASN cc_start: 0.7756 (t0) cc_final: 0.7416 (m110) outliers start: 65 outliers final: 37 residues processed: 261 average time/residue: 1.2103 time to fit residues: 361.5992 Evaluate side-chains 239 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 240 optimal weight: 0.5980 chunk 220 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 117 optimal weight: 0.0870 chunk 151 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 391 ASN A 475 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20594 Z= 0.179 Angle : 0.537 12.615 27765 Z= 0.277 Chirality : 0.039 0.219 2957 Planarity : 0.003 0.058 3536 Dihedral : 4.650 62.074 2670 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.34 % Allowed : 26.81 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.17), residues: 2383 helix: 1.36 (0.13), residues: 1536 sheet: -1.75 (0.61), residues: 44 loop : 0.03 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 958 HIS 0.019 0.001 HIS A 979 PHE 0.015 0.001 PHE B 699 TYR 0.026 0.001 TYR A 709 ARG 0.016 0.001 ARG B 677 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 204 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8279 (tp) REVERT: A 939 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7424 (mm110) REVERT: B 744 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8680 (t80) REVERT: B 776 ASP cc_start: 0.8246 (t70) cc_final: 0.8007 (t0) REVERT: B 936 MET cc_start: 0.3445 (OUTLIER) cc_final: 0.3050 (mpp) REVERT: B 976 MET cc_start: 0.4085 (mpm) cc_final: 0.3439 (mtm) REVERT: C 145 ARG cc_start: 0.7642 (tpp-160) cc_final: 0.6837 (mpp80) REVERT: D 233 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7511 (ptp90) REVERT: D 278 ASN cc_start: 0.7739 (t0) cc_final: 0.7401 (m110) outliers start: 52 outliers final: 37 residues processed: 244 average time/residue: 1.2414 time to fit residues: 345.3390 Evaluate side-chains 246 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 176 optimal weight: 20.0000 chunk 28 optimal weight: 0.4980 chunk 53 optimal weight: 7.9990 chunk 191 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 236 GLN D 202 ASN D 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093639 restraints weight = 30881.163| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.25 r_work: 0.3138 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20594 Z= 0.205 Angle : 0.539 12.296 27765 Z= 0.279 Chirality : 0.040 0.219 2957 Planarity : 0.004 0.071 3536 Dihedral : 4.652 61.781 2670 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.43 % Allowed : 26.63 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.17), residues: 2383 helix: 1.32 (0.13), residues: 1539 sheet: -1.73 (0.61), residues: 44 loop : 0.02 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 958 HIS 0.019 0.001 HIS A 979 PHE 0.016 0.001 PHE B 699 TYR 0.026 0.001 TYR A 709 ARG 0.010 0.001 ARG A 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7575.18 seconds wall clock time: 133 minutes 33.69 seconds (8013.69 seconds total)