Starting phenix.real_space_refine on Thu Aug 8 06:44:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyc_37923/08_2024/8wyc_37923_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyc_37923/08_2024/8wyc_37923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyc_37923/08_2024/8wyc_37923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyc_37923/08_2024/8wyc_37923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyc_37923/08_2024/8wyc_37923_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyc_37923/08_2024/8wyc_37923_neut.cif" } resolution = 3.0 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= 0.081 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 81 5.16 5 C 14440 2.51 5 N 3603 2.21 5 O 4253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 986": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 369": "OE1" <-> "OE2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 518": "OE1" <-> "OE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B GLU 759": "OE1" <-> "OE2" Residue "B GLU 766": "OE1" <-> "OE2" Residue "B GLU 890": "OE1" <-> "OE2" Residue "B GLU 998": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "G GLU 174": "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: 22385 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7940 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 19, 'TRANS': 932} Chain breaks: 6 Chain: "B" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7968 Classifications: {'peptide': 955} Link IDs: {'PTRANS': 19, 'TRANS': 935} Chain breaks: 5 Chain: "C" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2218 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 9, 'TRANS': 261} Chain breaks: 1 Chain: "D" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2231 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 10, 'TRANS': 262} Chain breaks: 1 Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 4 Chain: "G" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 913 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 5 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.34, per 1000 atoms: 0.64 Number of scatterers: 22385 At special positions: 0 Unit cell: (99.24, 126.531, 177.805, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 81 16.00 P 8 15.00 O 4253 8.00 N 3603 7.00 C 14440 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: 9.13 Conformation dependent library (CDL) restraints added in 3.8 seconds 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5114 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 12 sheets defined 64.0% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.989A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 Processing helix chain 'A' and resid 80 through 96 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.938A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 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: 3.927A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.732A pdb=" N ILE A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.605A pdb=" N ARG A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.721A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.596A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 removed outlier: 3.518A pdb=" N LYS A 372 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.533A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.694A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 468 through 494 Processing helix chain 'A' and resid 494 through 499 removed outlier: 3.823A pdb=" N LEU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 542 through 546 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 616 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.574A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.816A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 765 removed outlier: 4.239A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 3.872A 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 813 removed outlier: 4.043A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 831 through 840 removed outlier: 3.763A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 857 removed outlier: 4.239A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 878 through 897 Processing helix chain 'A' and resid 911 through 922 Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 940 through 945 Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 955 through 961 Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 976 through 991 removed outlier: 3.682A pdb=" N VAL A 980 " --> pdb=" O MET A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 Processing helix chain 'B' and resid 24 through 39 Processing helix chain 'B' and resid 47 through 54 removed outlier: 4.185A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.686A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.616A pdb=" N PHE B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.620A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.825A pdb=" N VAL B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.582A 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 235 removed outlier: 3.674A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.760A pdb=" N ILE B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.913A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.786A pdb=" N SER B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 392 removed outlier: 3.504A pdb=" N ALA B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.543A pdb=" N LYS B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 468 through 501 removed outlier: 3.629A pdb=" N TYR B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 520 Processing helix chain 'B' and resid 524 through 528 removed outlier: 4.261A pdb=" N PHE B 528 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 542 through 547 removed outlier: 3.816A pdb=" N SER B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 547' Processing helix chain 'B' and resid 551 through 572 Processing helix chain 'B' and resid 579 through 598 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 616 Processing helix chain 'B' and resid 618 through 628 removed outlier: 3.558A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) 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 removed outlier: 3.562A pdb=" N LYS B 675 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 676 " --> pdb=" O ILE B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 676' Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.040A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.576A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.741A 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 742 Processing helix chain 'B' and resid 750 through 765 removed outlier: 4.311A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 813 removed outlier: 3.572A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 827 Processing helix chain 'B' and resid 831 through 841 removed outlier: 3.657A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 841 " --> pdb=" O PHE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 846 through 857 removed outlier: 4.171A 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 897 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 929 through 934 Processing helix chain 'B' and resid 940 through 945 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: 3.892A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 962 " --> pdb=" O TRP B 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 962' Processing helix chain 'B' and resid 963 through 974 removed outlier: 4.543A pdb=" N LYS B 974 " --> pdb=" O ILE B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 991 removed outlier: 3.553A pdb=" N VAL B 980 " --> pdb=" O MET B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1004 removed outlier: 3.509A pdb=" N GLU B 998 " --> pdb=" O LYS B 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 39 Processing helix chain 'C' and resid 47 through 54 removed outlier: 3.886A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 53 " --> pdb=" O GLY C 49 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 removed outlier: 3.673A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 108 removed outlier: 3.862A pdb=" N LEU C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 7.004A pdb=" N GLU C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N MET C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.881A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.559A 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 154 through 160 removed outlier: 3.826A pdb=" N VAL C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 160' 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: 4.124A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 263 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 298 Processing helix chain 'D' and resid 26 through 40 Processing helix chain 'D' and resid 47 through 54 removed outlier: 3.942A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.516A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 95 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: 3.954A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 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 235 Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.565A pdb=" N ARG D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 77 Processing helix chain 'G' and resid 69 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.226A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 Processing sheet with id=AA4, first strand: chain 'B' and resid 906 through 907 removed outlier: 3.878A pdb=" N ASP E 10 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE E 23 " --> pdb=" O PHE E 13 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ARG E 15 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU E 21 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR E 29 " --> pdb=" O THR E 62 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS E 219 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 794 through 795 Processing sheet with id=AA6, first strand: chain 'A' and resid 906 through 908 removed outlier: 5.932A pdb=" N ARG G 15 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU G 21 " --> pdb=" O ARG G 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 906 through 908 removed outlier: 5.932A pdb=" N ARG G 15 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU G 21 " --> pdb=" O ARG G 15 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL G 22 " --> pdb=" O PHE G 68 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE G 68 " --> pdb=" O VAL G 22 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR G 24 " --> pdb=" O ALA G 66 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA G 66 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR G 62 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA G 30 " --> pdb=" O ASN G 60 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN G 60 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE G 32 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU G 58 " --> pdb=" O PHE G 32 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLN G 34 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU G 56 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE G 59 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS G 219 " --> pdb=" O SER G 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.682A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AB1, first strand: chain 'B' and resid 794 through 795 removed outlier: 3.596A pdb=" N SER B 795 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 150 through 152 removed outlier: 3.925A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE C 213 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE C 246 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE C 215 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.908A pdb=" N LEU D 42 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE D 130 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL D 43 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE D 216 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE D 45 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) 1190 hydrogen bonds defined for protein. 3420 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: 10.18 Time building geometry restraints manager: 10.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3776 1.32 - 1.44: 6403 1.44 - 1.57: 12576 1.57 - 1.69: 3 1.69 - 1.82: 139 Bond restraints: 22897 Sorted by residual: bond pdb=" O3 NAD B1101 " pdb=" PA NAD B1101 " ideal model delta sigma weight residual 1.653 1.498 0.155 2.00e-02 2.50e+03 5.98e+01 bond pdb=" O3 NAD C1101 " pdb=" PA NAD C1101 " ideal model delta sigma weight residual 1.653 1.502 0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" O3 NAD B1101 " pdb=" PN NAD B1101 " ideal model delta sigma weight residual 1.633 1.488 0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" O3 NAD D1101 " pdb=" PN NAD D1101 " ideal model delta sigma weight residual 1.633 1.501 0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" O3 NAD A1101 " pdb=" PN NAD A1101 " ideal model delta sigma weight residual 1.633 1.508 0.125 2.00e-02 2.50e+03 3.91e+01 ... (remaining 22892 not shown) Histogram of bond angle deviations from ideal: 75.97 - 88.47: 4 88.47 - 100.97: 59 100.97 - 113.47: 12422 113.47 - 125.97: 18174 125.97 - 138.46: 245 Bond angle restraints: 30904 Sorted by residual: angle pdb=" C1B NAD B1101 " pdb=" C2B NAD B1101 " pdb=" O2B NAD B1101 " ideal model delta sigma weight residual 113.98 75.97 38.01 3.00e+00 1.11e-01 1.60e+02 angle pdb=" C3B NAD B1101 " pdb=" C4B NAD B1101 " pdb=" C5B NAD B1101 " ideal model delta sigma weight residual 114.14 82.91 31.23 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C1B NAD C1101 " pdb=" C2B NAD C1101 " pdb=" O2B NAD C1101 " ideal model delta sigma weight residual 113.98 90.00 23.98 3.00e+00 1.11e-01 6.39e+01 angle pdb=" C3B NAD A1101 " pdb=" C4B NAD A1101 " pdb=" C5B NAD A1101 " ideal model delta sigma weight residual 114.14 91.74 22.40 3.00e+00 1.11e-01 5.57e+01 angle pdb=" O3 NAD C1101 " pdb=" PA NAD C1101 " pdb=" O5B NAD C1101 " ideal model delta sigma weight residual 101.67 81.79 19.88 3.00e+00 1.11e-01 4.39e+01 ... (remaining 30899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 11154 18.01 - 36.03: 1788 36.03 - 54.04: 628 54.04 - 72.06: 144 72.06 - 90.07: 35 Dihedral angle restraints: 13749 sinusoidal: 5809 harmonic: 7940 Sorted by residual: dihedral pdb=" CA LEU D 53 " pdb=" C LEU D 53 " pdb=" N SER D 54 " pdb=" CA SER D 54 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C CYS B 367 " pdb=" N CYS B 367 " pdb=" CA CYS B 367 " pdb=" CB CYS B 367 " ideal model delta harmonic sigma weight residual -122.60 -132.22 9.62 0 2.50e+00 1.60e-01 1.48e+01 dihedral pdb=" CA SER A 615 " pdb=" C SER A 615 " pdb=" N MET A 616 " pdb=" CA MET A 616 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 13746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 3293 0.151 - 0.301: 11 0.301 - 0.452: 2 0.452 - 0.602: 1 0.602 - 0.753: 2 Chirality restraints: 3309 Sorted by residual: chirality pdb=" C3B NAD B1101 " pdb=" C2B NAD B1101 " pdb=" C4B NAD B1101 " pdb=" O3B NAD B1101 " both_signs ideal model delta sigma weight residual False -2.71 -1.96 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C1B NAD B1101 " pdb=" C2B NAD B1101 " pdb=" N9A NAD B1101 " pdb=" O4B NAD B1101 " both_signs ideal model delta sigma weight residual False 2.35 1.71 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C3B NAD A1101 " pdb=" C2B NAD A1101 " pdb=" C4B NAD A1101 " pdb=" O3B NAD A1101 " both_signs ideal model delta sigma weight residual False -2.71 -2.23 -0.48 2.00e-01 2.50e+01 5.83e+00 ... (remaining 3306 not shown) Planarity restraints: 3916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 251 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO D 252 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 252 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 252 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 366 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C SER B 366 " 0.049 2.00e-02 2.50e+03 pdb=" O SER B 366 " -0.018 2.00e-02 2.50e+03 pdb=" N CYS B 367 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 367 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C CYS B 367 " -0.045 2.00e-02 2.50e+03 pdb=" O CYS B 367 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP B 368 " 0.016 2.00e-02 2.50e+03 ... (remaining 3913 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 204 2.47 - 3.08: 16733 3.08 - 3.68: 34520 3.68 - 4.29: 53684 4.29 - 4.90: 89951 Nonbonded interactions: 195092 Sorted by model distance: nonbonded pdb=" OH TYR A 286 " pdb=" O2B NAD A1101 " model vdw 1.861 3.040 nonbonded pdb=" OE2 GLU B 685 " pdb=" OG SER B 729 " model vdw 1.997 3.040 nonbonded pdb=" OG SER D 51 " pdb=" OD2 ASP D 135 " model vdw 2.000 3.040 nonbonded pdb=" OH TYR A 414 " pdb=" OD1 ASN A 654 " model vdw 2.018 3.040 nonbonded pdb=" NH1 ARG D 247 " pdb=" OD1 ASP D 249 " model vdw 2.018 3.120 ... (remaining 195087 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 23 through 74 or resid 79 through 463 or resid 467 through \ 633 or resid 644 through 1005 or resid 1101)) selection = (chain 'B' and (resid 23 through 296 or resid 304 through 365 or resid 369 throu \ gh 786 or resid 789 through 1005 or resid 1101)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 22 through 72 or resid 79 through 298 or resid 1101)) } ncs_group { reference = (chain 'E' and (resid 8 through 36 or resid 41 through 236)) selection = (chain 'G' and (resid 8 through 176 or resid 191 through 236)) } 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: 18.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 65.530 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 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: 0.020 Load rotamer database and sin/cos tables:16.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 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 : 0.005 0.155 22897 Z= 0.329 Angle : 0.806 38.005 30904 Z= 0.353 Chirality : 0.044 0.753 3309 Planarity : 0.003 0.077 3916 Dihedral : 20.078 90.074 8635 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 38.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 6.67 % Allowed : 35.37 % Favored : 57.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2624 helix: 1.47 (0.14), residues: 1519 sheet: -0.26 (0.44), residues: 123 loop : -0.76 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 60 HIS 0.005 0.001 HIS A 978 PHE 0.019 0.001 PHE G 23 TYR 0.014 0.001 TYR C 92 ARG 0.005 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 353 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 930 MET cc_start: 0.6758 (mtt) cc_final: 0.6486 (mtt) REVERT: C 35 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7683 (tm-30) REVERT: D 185 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7499 (pp) REVERT: G 227 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7272 (m-30) outliers start: 163 outliers final: 141 residues processed: 503 average time/residue: 1.0413 time to fit residues: 617.1379 Evaluate side-chains 481 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 338 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 821 SER Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 834 GLN Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 907 PHE Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 234 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.1980 chunk 201 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 241 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 GLN A 832 GLN A 910 ASN B 25 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN B 491 GLN ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 ASN C 196 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN G 197 ASN G 210 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22897 Z= 0.252 Angle : 0.626 10.975 30904 Z= 0.329 Chirality : 0.044 0.214 3309 Planarity : 0.004 0.077 3916 Dihedral : 11.696 88.606 3402 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 7.94 % Allowed : 29.64 % Favored : 62.42 % 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: 0.38 (0.16), residues: 2624 helix: 1.03 (0.13), residues: 1552 sheet: -0.43 (0.43), residues: 122 loop : -0.89 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 60 HIS 0.007 0.001 HIS A 67 PHE 0.021 0.002 PHE E 23 TYR 0.021 0.002 TYR A 951 ARG 0.006 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 373 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6021 (mp0) REVERT: A 316 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 457 ASN cc_start: 0.8434 (t0) cc_final: 0.7935 (m110) REVERT: A 602 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8420 (p) REVERT: A 1003 TYR cc_start: 0.6658 (OUTLIER) cc_final: 0.4250 (p90) REVERT: B 25 ASN cc_start: 0.7393 (t0) cc_final: 0.6972 (t0) REVERT: B 35 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: B 98 MET cc_start: 0.7959 (mmm) cc_final: 0.7544 (mpp) REVERT: B 278 ASN cc_start: 0.7482 (p0) cc_final: 0.6436 (t0) REVERT: B 434 ASP cc_start: 0.8127 (t0) cc_final: 0.7715 (m-30) REVERT: B 516 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: B 543 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: B 564 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8244 (mtmt) REVERT: B 982 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6932 (mt-10) REVERT: C 98 MET cc_start: 0.7123 (mmm) cc_final: 0.6260 (mmm) REVERT: C 280 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6630 (t80) REVERT: D 54 SER cc_start: 0.5935 (OUTLIER) cc_final: 0.5467 (p) REVERT: D 185 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7284 (pp) REVERT: D 247 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7309 (tmm160) REVERT: E 48 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6556 (ptmm) REVERT: E 52 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7650 (mp) REVERT: G 14 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8020 (ptpp) REVERT: G 208 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7974 (pt) outliers start: 194 outliers final: 72 residues processed: 523 average time/residue: 1.1360 time to fit residues: 692.7964 Evaluate side-chains 412 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 324 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 764 CYS Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 907 PHE Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 234 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 241 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 82 optimal weight: 0.0970 chunk 194 optimal weight: 3.9990 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 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 765 ASN A 910 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22897 Z= 0.221 Angle : 0.569 9.351 30904 Z= 0.301 Chirality : 0.042 0.176 3309 Planarity : 0.004 0.077 3916 Dihedral : 9.972 83.368 3249 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 7.08 % Allowed : 29.55 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2624 helix: 0.94 (0.13), residues: 1546 sheet: -0.41 (0.45), residues: 120 loop : -0.92 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 60 HIS 0.010 0.001 HIS A 67 PHE 0.017 0.002 PHE E 23 TYR 0.026 0.002 TYR A 951 ARG 0.007 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 353 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8049 (mpp) cc_final: 0.7848 (mpm) REVERT: A 254 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6069 (mp0) REVERT: A 316 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8502 (mp) REVERT: A 457 ASN cc_start: 0.8378 (t0) cc_final: 0.7923 (m-40) REVERT: A 574 TYR cc_start: 0.8598 (m-80) cc_final: 0.8360 (m-80) REVERT: A 602 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8394 (p) REVERT: A 930 MET cc_start: 0.7411 (mtp) cc_final: 0.7119 (mtt) REVERT: A 1003 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.4793 (p90) REVERT: B 25 ASN cc_start: 0.7360 (t0) cc_final: 0.6967 (t0) REVERT: B 35 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: B 64 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: B 98 MET cc_start: 0.7889 (mmm) cc_final: 0.7404 (mpp) REVERT: B 278 ASN cc_start: 0.7469 (p0) cc_final: 0.6342 (t0) REVERT: B 284 GLU cc_start: 0.7490 (mp0) cc_final: 0.7280 (mp0) REVERT: B 516 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: B 543 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8307 (tp30) REVERT: B 564 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8213 (mtmt) REVERT: B 618 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8834 (tp) REVERT: C 98 MET cc_start: 0.7250 (mmm) cc_final: 0.6490 (mmm) REVERT: C 280 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6733 (m-80) REVERT: D 98 MET cc_start: 0.7665 (tpp) cc_final: 0.7414 (tpt) REVERT: D 184 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8669 (m) REVERT: D 247 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7312 (tmm160) REVERT: D 262 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: E 52 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7632 (mp) REVERT: E 54 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7156 (mmtp) REVERT: E 214 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5737 (mm) REVERT: G 14 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8050 (ptpp) REVERT: G 208 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8030 (pt) outliers start: 173 outliers final: 64 residues processed: 485 average time/residue: 1.1224 time to fit residues: 635.3348 Evaluate side-chains 398 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 315 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 907 PHE Chi-restraints excluded: chain B residue 910 ASN Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 233 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 0.0670 chunk 181 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 257 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 230 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN A 910 ASN B 765 ASN ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 ASN C 160 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 HIS D 236 GLN E 60 ASN G 197 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22897 Z= 0.228 Angle : 0.560 8.476 30904 Z= 0.298 Chirality : 0.042 0.311 3309 Planarity : 0.004 0.075 3916 Dihedral : 9.266 79.728 3218 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 7.04 % Allowed : 29.72 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2624 helix: 0.86 (0.13), residues: 1553 sheet: -0.55 (0.45), residues: 120 loop : -0.97 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 60 HIS 0.005 0.001 HIS D 128 PHE 0.018 0.002 PHE A 877 TYR 0.022 0.001 TYR A 951 ARG 0.008 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 342 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8082 (mptp) REVERT: A 98 MET cc_start: 0.8039 (mpp) cc_final: 0.7672 (mpp) REVERT: A 254 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: A 316 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8520 (mp) REVERT: A 374 SER cc_start: 0.6195 (OUTLIER) cc_final: 0.5991 (t) REVERT: A 457 ASN cc_start: 0.8427 (t0) cc_final: 0.7944 (m-40) REVERT: A 574 TYR cc_start: 0.8626 (m-80) cc_final: 0.8425 (m-80) REVERT: A 602 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8341 (p) REVERT: B 25 ASN cc_start: 0.7368 (t0) cc_final: 0.6978 (t0) REVERT: B 35 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: B 64 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: B 98 MET cc_start: 0.7804 (mmm) cc_final: 0.7350 (mpp) REVERT: B 284 GLU cc_start: 0.7490 (mp0) cc_final: 0.7262 (mp0) REVERT: B 434 ASP cc_start: 0.8056 (t0) cc_final: 0.7634 (m-30) REVERT: B 516 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: B 543 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: B 564 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8215 (mtmt) REVERT: B 618 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8829 (tp) REVERT: C 98 MET cc_start: 0.7086 (mmm) cc_final: 0.6403 (mmm) REVERT: C 280 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: C 290 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.7034 (mmt) REVERT: D 185 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7283 (pp) REVERT: D 227 MET cc_start: 0.7948 (mmm) cc_final: 0.7727 (mmt) REVERT: D 235 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7701 (mp) REVERT: D 262 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: E 52 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7532 (mp) REVERT: E 54 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7138 (mmtp) REVERT: E 203 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: G 51 TYR cc_start: 0.7698 (t80) cc_final: 0.7114 (t80) REVERT: G 208 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8136 (pt) outliers start: 172 outliers final: 65 residues processed: 473 average time/residue: 1.0869 time to fit residues: 603.9965 Evaluate side-chains 403 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 318 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 907 PHE Chi-restraints excluded: chain B residue 910 ASN Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain G residue 233 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 131 optimal weight: 0.5980 chunk 230 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 711 GLN A 765 ASN A 910 ASN A 979 HIS B 89 GLN B 765 ASN ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN G 197 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22897 Z= 0.243 Angle : 0.565 10.216 30904 Z= 0.300 Chirality : 0.042 0.225 3309 Planarity : 0.004 0.045 3916 Dihedral : 8.838 76.264 3200 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.75 % Allowed : 29.43 % Favored : 63.81 % 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: 0.13 (0.16), residues: 2624 helix: 0.82 (0.13), residues: 1550 sheet: -0.74 (0.43), residues: 130 loop : -0.92 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 60 HIS 0.005 0.001 HIS A 67 PHE 0.015 0.002 PHE E 23 TYR 0.024 0.001 TYR A 951 ARG 0.008 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 330 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8096 (mptp) REVERT: A 69 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: A 98 MET cc_start: 0.8030 (mpp) cc_final: 0.7665 (mpp) REVERT: A 254 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6012 (mp0) REVERT: A 316 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8531 (mp) REVERT: A 374 SER cc_start: 0.6221 (OUTLIER) cc_final: 0.5997 (t) REVERT: A 457 ASN cc_start: 0.8400 (t0) cc_final: 0.7948 (m-40) REVERT: A 873 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8218 (tp) REVERT: B 25 ASN cc_start: 0.7368 (t0) cc_final: 0.6981 (t0) REVERT: B 35 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: B 64 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: B 98 MET cc_start: 0.7789 (mmm) cc_final: 0.7354 (mpp) REVERT: B 106 ASP cc_start: 0.6995 (m-30) cc_final: 0.6788 (m-30) REVERT: B 187 GLU cc_start: 0.7661 (tt0) cc_final: 0.7419 (tt0) REVERT: B 284 GLU cc_start: 0.7490 (mp0) cc_final: 0.7267 (mp0) REVERT: B 339 HIS cc_start: 0.8174 (t-90) cc_final: 0.7862 (t-90) REVERT: B 358 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: B 434 ASP cc_start: 0.8049 (t0) cc_final: 0.7613 (m-30) REVERT: B 516 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: B 543 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8326 (tp30) REVERT: B 564 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8214 (mtmt) REVERT: C 98 MET cc_start: 0.6950 (mmm) cc_final: 0.6316 (mmm) REVERT: C 280 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6520 (t80) REVERT: D 106 ASP cc_start: 0.7792 (m-30) cc_final: 0.7542 (m-30) REVERT: D 185 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7358 (pp) REVERT: D 227 MET cc_start: 0.7950 (mmm) cc_final: 0.7734 (mmt) REVERT: D 262 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: E 52 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7561 (mp) REVERT: E 54 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7174 (mmtp) REVERT: E 191 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6401 (pp) REVERT: E 214 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5685 (mm) REVERT: G 208 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8180 (pt) outliers start: 165 outliers final: 78 residues processed: 458 average time/residue: 1.0674 time to fit residues: 576.0943 Evaluate side-chains 413 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 315 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 104 LEU 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 358 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 907 PHE Chi-restraints excluded: chain B residue 910 ASN Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain G residue 233 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 257 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 ASN A 979 HIS B 765 ASN B 927 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN G 197 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22897 Z= 0.230 Angle : 0.553 9.383 30904 Z= 0.294 Chirality : 0.041 0.206 3309 Planarity : 0.004 0.046 3916 Dihedral : 8.495 72.472 3193 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.55 % Allowed : 29.59 % Favored : 63.86 % 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: 0.14 (0.16), residues: 2624 helix: 0.82 (0.13), residues: 1554 sheet: -0.77 (0.43), residues: 130 loop : -0.92 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 60 HIS 0.005 0.001 HIS A 979 PHE 0.018 0.002 PHE B 576 TYR 0.023 0.001 TYR A 951 ARG 0.007 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 333 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8067 (mptp) REVERT: A 69 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: A 98 MET cc_start: 0.8029 (mpp) cc_final: 0.7682 (mpp) REVERT: A 316 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8525 (mp) REVERT: A 317 SER cc_start: 0.8892 (t) cc_final: 0.8621 (t) REVERT: A 374 SER cc_start: 0.6125 (OUTLIER) cc_final: 0.5916 (t) REVERT: A 435 ASP cc_start: 0.8108 (t70) cc_final: 0.7555 (m-30) REVERT: A 457 ASN cc_start: 0.8367 (t0) cc_final: 0.7948 (m-40) REVERT: A 574 TYR cc_start: 0.8572 (m-80) cc_final: 0.8349 (m-80) REVERT: A 857 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.6982 (mmmt) REVERT: B 25 ASN cc_start: 0.7369 (t0) cc_final: 0.6969 (t0) REVERT: B 35 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: B 64 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: B 98 MET cc_start: 0.7797 (mmm) cc_final: 0.7378 (mpp) REVERT: B 187 GLU cc_start: 0.7671 (tt0) cc_final: 0.7414 (tt0) REVERT: B 284 GLU cc_start: 0.7495 (mp0) cc_final: 0.7269 (mp0) REVERT: B 310 ASP cc_start: 0.7662 (m-30) cc_final: 0.7299 (m-30) REVERT: B 339 HIS cc_start: 0.8132 (t-90) cc_final: 0.7850 (t-90) REVERT: B 434 ASP cc_start: 0.8008 (t0) cc_final: 0.7588 (m-30) REVERT: B 516 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: B 543 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8304 (tp30) REVERT: B 564 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8254 (mtmt) REVERT: B 856 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.5342 (m-80) REVERT: C 98 MET cc_start: 0.6980 (mmm) cc_final: 0.6295 (mmm) REVERT: C 145 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6774 (tmm160) REVERT: C 277 SER cc_start: 0.8151 (OUTLIER) cc_final: 0.7918 (m) REVERT: C 280 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: C 290 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6980 (mmt) REVERT: D 106 ASP cc_start: 0.7829 (m-30) cc_final: 0.7590 (m-30) REVERT: D 124 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8744 (mmt) REVERT: D 227 MET cc_start: 0.7963 (mmm) cc_final: 0.7759 (mmt) REVERT: D 235 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7683 (mp) REVERT: D 262 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: E 39 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: E 52 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7527 (mt) REVERT: E 54 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7097 (mmtp) REVERT: E 203 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7041 (tp30) REVERT: G 51 TYR cc_start: 0.7698 (t80) cc_final: 0.7136 (t80) REVERT: G 208 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8203 (pt) outliers start: 160 outliers final: 75 residues processed: 453 average time/residue: 1.0771 time to fit residues: 574.2577 Evaluate side-chains 412 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 314 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 104 LEU 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 430 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 856 PHE Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain B residue 910 ASN Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain G residue 233 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 187 optimal weight: 0.0470 chunk 145 optimal weight: 0.6980 chunk 216 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN A 979 HIS B 609 HIS B 765 ASN B 927 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22897 Z= 0.196 Angle : 0.553 11.440 30904 Z= 0.294 Chirality : 0.041 0.191 3309 Planarity : 0.004 0.044 3916 Dihedral : 8.212 73.250 3185 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.44 % Allowed : 30.62 % Favored : 63.94 % 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: 0.18 (0.16), residues: 2624 helix: 0.87 (0.13), residues: 1554 sheet: -0.74 (0.44), residues: 130 loop : -0.93 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 60 HIS 0.007 0.001 HIS A 979 PHE 0.018 0.001 PHE A 381 TYR 0.025 0.001 TYR A 951 ARG 0.009 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 334 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7958 (mtpp) REVERT: A 98 MET cc_start: 0.8023 (mpp) cc_final: 0.7679 (mpp) REVERT: A 316 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8537 (mp) REVERT: A 317 SER cc_start: 0.8884 (t) cc_final: 0.8623 (t) REVERT: A 435 ASP cc_start: 0.8113 (t70) cc_final: 0.7555 (m-30) REVERT: A 457 ASN cc_start: 0.8345 (t0) cc_final: 0.7942 (m-40) REVERT: A 574 TYR cc_start: 0.8596 (m-80) cc_final: 0.8385 (m-80) REVERT: A 602 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8319 (p) REVERT: A 913 MET cc_start: 0.7025 (mtp) cc_final: 0.6819 (ttt) REVERT: B 25 ASN cc_start: 0.7344 (t0) cc_final: 0.6948 (t0) REVERT: B 35 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: B 64 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7431 (m-30) REVERT: B 98 MET cc_start: 0.7754 (mmm) cc_final: 0.7341 (mpp) REVERT: B 187 GLU cc_start: 0.7650 (tt0) cc_final: 0.7327 (tt0) REVERT: B 284 GLU cc_start: 0.7478 (mp0) cc_final: 0.7245 (mp0) REVERT: B 339 HIS cc_start: 0.8098 (t-90) cc_final: 0.7785 (t-90) REVERT: B 389 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: B 434 ASP cc_start: 0.7959 (t0) cc_final: 0.7573 (m-30) REVERT: B 516 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: B 543 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8279 (tp30) REVERT: B 564 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8220 (mtmt) REVERT: B 618 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8648 (tp) REVERT: C 98 MET cc_start: 0.6970 (mmm) cc_final: 0.6326 (mmm) REVERT: C 280 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: C 290 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6935 (mmt) REVERT: D 124 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8746 (mmt) REVERT: D 262 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: E 52 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7558 (mt) REVERT: E 54 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7074 (mmtp) REVERT: E 191 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6605 (pp) REVERT: E 203 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7031 (tp30) REVERT: E 214 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5644 (mm) REVERT: G 51 TYR cc_start: 0.7710 (t80) cc_final: 0.7126 (t80) REVERT: G 208 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8181 (pt) outliers start: 133 outliers final: 70 residues processed: 429 average time/residue: 1.0481 time to fit residues: 528.5695 Evaluate side-chains 401 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 311 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 104 LEU 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 389 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 731 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain B residue 910 ASN Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain G residue 233 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 0.0010 chunk 102 optimal weight: 0.0270 chunk 153 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 162 optimal weight: 0.5980 chunk 174 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 overall best weight: 0.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN A 979 HIS B 765 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN G 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22897 Z= 0.179 Angle : 0.544 10.066 30904 Z= 0.290 Chirality : 0.041 0.182 3309 Planarity : 0.003 0.043 3916 Dihedral : 8.050 74.937 3185 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.20 % Allowed : 31.44 % Favored : 63.36 % 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: 0.22 (0.16), residues: 2624 helix: 0.90 (0.13), residues: 1554 sheet: -0.71 (0.45), residues: 130 loop : -0.93 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 60 HIS 0.008 0.001 HIS A 979 PHE 0.018 0.001 PHE G 67 TYR 0.030 0.001 TYR A 951 ARG 0.008 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 330 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: A 76 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8110 (tptp) REVERT: A 98 MET cc_start: 0.8021 (mpp) cc_final: 0.7625 (mpp) REVERT: A 316 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8539 (mp) REVERT: A 317 SER cc_start: 0.8872 (t) cc_final: 0.8605 (t) REVERT: A 435 ASP cc_start: 0.8097 (t70) cc_final: 0.7521 (m-30) REVERT: A 457 ASN cc_start: 0.8323 (t0) cc_final: 0.7938 (m-40) REVERT: A 857 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.6962 (mmmt) REVERT: B 25 ASN cc_start: 0.7310 (t0) cc_final: 0.6915 (t0) REVERT: B 35 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: B 64 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: B 98 MET cc_start: 0.7748 (mmm) cc_final: 0.7360 (mpp) REVERT: B 187 GLU cc_start: 0.7645 (tt0) cc_final: 0.7319 (tt0) REVERT: B 284 GLU cc_start: 0.7495 (mp0) cc_final: 0.7249 (mp0) REVERT: B 339 HIS cc_start: 0.8116 (t-90) cc_final: 0.7778 (t-90) REVERT: B 389 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: B 434 ASP cc_start: 0.7945 (t0) cc_final: 0.7539 (m-30) REVERT: B 516 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: B 543 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: B 618 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8649 (tp) REVERT: B 856 PHE cc_start: 0.6513 (OUTLIER) cc_final: 0.5133 (m-80) REVERT: C 28 GLU cc_start: 0.5633 (tp30) cc_final: 0.5401 (tp30) REVERT: C 98 MET cc_start: 0.6871 (mmm) cc_final: 0.6262 (mmm) REVERT: C 145 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6878 (tmm160) REVERT: C 277 SER cc_start: 0.8112 (OUTLIER) cc_final: 0.7874 (m) REVERT: C 280 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: C 290 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6924 (mmt) REVERT: D 98 MET cc_start: 0.7488 (tpp) cc_final: 0.7049 (tpt) REVERT: D 107 PHE cc_start: 0.8181 (t80) cc_final: 0.7853 (t80) REVERT: D 124 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8740 (mmt) REVERT: D 227 MET cc_start: 0.7993 (mmm) cc_final: 0.7788 (mmt) REVERT: D 262 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: E 52 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7637 (mt) REVERT: E 54 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7056 (mmtp) REVERT: E 203 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7013 (tp30) REVERT: E 214 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5656 (mm) REVERT: G 208 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8126 (pt) outliers start: 127 outliers final: 65 residues processed: 424 average time/residue: 1.0745 time to fit residues: 537.1823 Evaluate side-chains 392 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 305 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 104 LEU 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 389 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 731 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 856 PHE Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 910 ASN Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain G residue 233 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.5980 chunk 245 optimal weight: 0.7980 chunk 224 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN A 979 HIS B 226 ASN B 263 ASN B 765 ASN D 128 HIS D 236 GLN E 65 ASN E 194 GLN G 65 ASN G 197 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22897 Z= 0.248 Angle : 0.584 10.083 30904 Z= 0.309 Chirality : 0.042 0.187 3309 Planarity : 0.004 0.049 3916 Dihedral : 7.913 75.596 3181 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.54 % Allowed : 32.75 % Favored : 62.71 % 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: 0.09 (0.16), residues: 2624 helix: 0.79 (0.13), residues: 1561 sheet: -0.74 (0.44), residues: 130 loop : -0.98 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 60 HIS 0.009 0.001 HIS A 979 PHE 0.034 0.002 PHE G 23 TYR 0.017 0.001 TYR A 951 ARG 0.009 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 311 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8044 (mptp) REVERT: A 69 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: A 76 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7995 (mtpp) REVERT: A 98 MET cc_start: 0.8044 (mpp) cc_final: 0.7719 (mpp) REVERT: A 316 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8507 (mp) REVERT: A 317 SER cc_start: 0.8909 (t) cc_final: 0.8654 (t) REVERT: A 435 ASP cc_start: 0.8155 (t70) cc_final: 0.7588 (m-30) REVERT: A 457 ASN cc_start: 0.8345 (t0) cc_final: 0.7958 (m-40) REVERT: A 857 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.6986 (mmmt) REVERT: B 25 ASN cc_start: 0.7336 (t0) cc_final: 0.6942 (t0) REVERT: B 35 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: B 64 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: B 98 MET cc_start: 0.7722 (mmm) cc_final: 0.7328 (mpp) REVERT: B 187 GLU cc_start: 0.7673 (tt0) cc_final: 0.7345 (tt0) REVERT: B 284 GLU cc_start: 0.7510 (mp0) cc_final: 0.7256 (mp0) REVERT: B 339 HIS cc_start: 0.8119 (t-90) cc_final: 0.7870 (t-90) REVERT: B 389 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: B 434 ASP cc_start: 0.7927 (t0) cc_final: 0.7535 (m-30) REVERT: B 516 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: B 543 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8303 (tp30) REVERT: B 564 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8300 (mtmt) REVERT: B 951 TYR cc_start: 0.7388 (m-80) cc_final: 0.7166 (m-10) REVERT: C 98 MET cc_start: 0.6921 (mmm) cc_final: 0.6310 (mmm) REVERT: C 125 ASN cc_start: 0.8655 (t0) cc_final: 0.8157 (m110) REVERT: C 145 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6856 (tmm160) REVERT: C 277 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7893 (m) REVERT: C 280 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.6765 (m-80) REVERT: C 290 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6849 (mmt) REVERT: D 98 MET cc_start: 0.7535 (tpp) cc_final: 0.7135 (tpt) REVERT: D 124 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8756 (mmt) REVERT: D 262 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: E 52 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7616 (mt) REVERT: E 54 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7101 (mmtp) REVERT: E 203 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7006 (tp30) REVERT: E 214 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5697 (mm) REVERT: G 208 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8225 (pt) outliers start: 111 outliers final: 65 residues processed: 395 average time/residue: 1.1152 time to fit residues: 514.4165 Evaluate side-chains 385 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 298 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 731 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 910 ASN Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain G residue 234 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 265 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN A 979 HIS B 765 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN G 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22897 Z= 0.250 Angle : 0.588 9.988 30904 Z= 0.310 Chirality : 0.042 0.183 3309 Planarity : 0.004 0.047 3916 Dihedral : 7.776 76.848 3177 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.30 % Allowed : 32.87 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2624 helix: 0.76 (0.13), residues: 1557 sheet: -0.83 (0.45), residues: 130 loop : -1.02 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 60 HIS 0.009 0.001 HIS A 979 PHE 0.035 0.002 PHE G 23 TYR 0.031 0.001 TYR A 951 ARG 0.009 0.000 ARG B 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 302 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: A 76 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7963 (mtpp) REVERT: A 98 MET cc_start: 0.8085 (mpp) cc_final: 0.7750 (mpp) REVERT: A 316 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8509 (mp) REVERT: A 317 SER cc_start: 0.8922 (t) cc_final: 0.8675 (t) REVERT: A 435 ASP cc_start: 0.8176 (t70) cc_final: 0.7611 (m-30) REVERT: A 457 ASN cc_start: 0.8344 (t0) cc_final: 0.7960 (m-40) REVERT: A 857 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7056 (mmmt) REVERT: B 25 ASN cc_start: 0.7343 (t0) cc_final: 0.6948 (t0) REVERT: B 35 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: B 64 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7491 (m-30) REVERT: B 98 MET cc_start: 0.7720 (mmm) cc_final: 0.7343 (mpp) REVERT: B 187 GLU cc_start: 0.7672 (tt0) cc_final: 0.7356 (tt0) REVERT: B 284 GLU cc_start: 0.7512 (mp0) cc_final: 0.7266 (mp0) REVERT: B 339 HIS cc_start: 0.8158 (t-90) cc_final: 0.7886 (t-90) REVERT: B 389 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: B 434 ASP cc_start: 0.7922 (t0) cc_final: 0.7543 (m-30) REVERT: B 516 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: B 543 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8329 (tp30) REVERT: B 856 PHE cc_start: 0.6571 (OUTLIER) cc_final: 0.5186 (m-80) REVERT: B 951 TYR cc_start: 0.7430 (m-80) cc_final: 0.7222 (m-10) REVERT: C 98 MET cc_start: 0.6904 (mmm) cc_final: 0.6286 (mmm) REVERT: C 145 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6859 (tmm160) REVERT: C 277 SER cc_start: 0.8165 (OUTLIER) cc_final: 0.7910 (m) REVERT: C 280 TYR cc_start: 0.7063 (OUTLIER) cc_final: 0.6838 (m-80) REVERT: D 98 MET cc_start: 0.7492 (tpp) cc_final: 0.7118 (tpt) REVERT: D 124 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8748 (mmt) REVERT: D 262 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: E 52 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7648 (mt) REVERT: E 54 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7098 (mmtp) REVERT: E 192 TYR cc_start: 0.7262 (p90) cc_final: 0.6960 (p90) REVERT: E 203 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7024 (tp30) REVERT: E 214 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5681 (mm) REVERT: E 217 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7071 (mt-10) REVERT: G 208 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8322 (pt) outliers start: 105 outliers final: 63 residues processed: 383 average time/residue: 1.1475 time to fit residues: 515.3048 Evaluate side-chains 379 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 296 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 856 PHE Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 910 ASN Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain G residue 234 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 185 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN B 765 ASN D 128 HIS D 236 GLN G 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.166977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.133326 restraints weight = 25632.219| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.11 r_work: 0.3213 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22897 Z= 0.243 Angle : 0.588 9.956 30904 Z= 0.312 Chirality : 0.042 0.183 3309 Planarity : 0.004 0.047 3916 Dihedral : 7.668 77.621 3177 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.26 % Allowed : 33.20 % Favored : 62.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 2624 helix: 0.74 (0.13), residues: 1559 sheet: -0.83 (0.45), residues: 130 loop : -1.05 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 60 HIS 0.006 0.001 HIS A 978 PHE 0.037 0.002 PHE G 23 TYR 0.020 0.001 TYR C 92 ARG 0.009 0.000 ARG B 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9178.77 seconds wall clock time: 162 minutes 33.31 seconds (9753.31 seconds total)