Starting phenix.real_space_refine on Sun May 12 17:13:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyc_37923/05_2024/8wyc_37923_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyc_37923/05_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_37923/05_2024/8wyc_37923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyc_37923/05_2024/8wyc_37923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyc_37923/05_2024/8wyc_37923_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyc_37923/05_2024/8wyc_37923_neut_updated.pdb" } 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-5322/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: 11.09, per 1000 atoms: 0.50 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: 8.69 Conformation dependent library (CDL) restraints added in 3.6 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... running ksdssp... Secondary structure from input PDB file: 142 helices and 11 sheets defined 54.6% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'A' and resid 24 through 38 Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.707A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 71 Processing helix chain 'A' and resid 81 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.697A pdb=" N MET A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 193 through 196 No H-bonds generated for 'chain 'A' and resid 193 through 196' Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 223 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 255 through 262 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 274 No H-bonds generated for 'chain 'A' and resid 271 through 274' Processing helix chain 'A' and resid 282 through 294 removed outlier: 3.622A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 321 Proline residue: A 318 - end of helix removed outlier: 4.543A pdb=" N ALA A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 356 through 364 removed outlier: 3.596A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 418 through 426 Processing helix chain 'A' and resid 432 through 444 removed outlier: 3.694A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 4.379A pdb=" N ILE A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 493 Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 509 through 519 Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 552 through 571 Processing helix chain 'A' and resid 580 through 597 Processing helix chain 'A' and resid 601 through 604 Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 619 through 627 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 661 through 670 Processing helix chain 'A' and resid 681 through 700 Processing helix chain 'A' and resid 706 through 724 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) removed outlier: 4.602A pdb=" N LYS A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 741 Processing helix chain 'A' and resid 751 through 764 removed outlier: 4.239A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 785 Processing helix chain 'A' and resid 801 through 812 Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 832 through 844 removed outlier: 3.763A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Proline residue: A 843 - end of helix Processing helix chain 'A' and resid 847 through 856 removed outlier: 4.239A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 871 Processing helix chain 'A' and resid 879 through 896 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 930 through 933 Processing helix chain 'A' and resid 941 through 944 No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 951 through 953 No H-bonds generated for 'chain 'A' and resid 951 through 953' Processing helix chain 'A' and resid 956 through 960 Processing helix chain 'A' and resid 964 through 973 Processing helix chain 'A' and resid 977 through 990 Processing helix chain 'A' and resid 995 through 1003 Processing helix chain 'B' and resid 24 through 38 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.702A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 Processing helix chain 'B' and resid 81 through 95 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 97 through 108 removed outlier: 3.616A pdb=" N PHE B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 124 removed outlier: 3.650A pdb=" N MET B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.178A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 159' Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 193 through 196 No H-bonds generated for 'chain 'B' and resid 193 through 196' Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 223 through 234 removed outlier: 3.674A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 262 Processing helix chain 'B' and resid 271 through 274 No H-bonds generated for 'chain 'B' and resid 271 through 274' Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 305 through 321 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) Proline residue: B 318 - end of helix removed outlier: 4.482A pdb=" N ALA B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 356 through 365 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 375 through 391 removed outlier: 3.504A pdb=" N ALA B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 426 removed outlier: 3.543A pdb=" N LYS B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 444 Processing helix chain 'B' and resid 448 through 460 Processing helix chain 'B' and resid 469 through 500 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 509 through 519 Processing helix chain 'B' and resid 525 through 527 No H-bonds generated for 'chain 'B' and resid 525 through 527' Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 541 through 546 removed outlier: 4.082A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 571 Processing helix chain 'B' and resid 580 through 597 Processing helix chain 'B' and resid 601 through 604 Processing helix chain 'B' and resid 606 through 615 Processing helix chain 'B' and resid 619 through 627 Processing helix chain 'B' and resid 649 through 658 Processing helix chain 'B' and resid 661 through 670 Processing helix chain 'B' and resid 673 through 675 No H-bonds generated for 'chain 'B' and resid 673 through 675' Processing helix chain 'B' and resid 681 through 700 Processing helix chain 'B' and resid 706 through 725 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) removed outlier: 4.691A pdb=" N LYS B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N TYR B 725 " --> pdb=" O TYR B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 742 Processing helix chain 'B' and resid 751 through 764 removed outlier: 4.311A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 785 Processing helix chain 'B' and resid 801 through 812 Processing helix chain 'B' and resid 818 through 826 Processing helix chain 'B' and resid 832 through 840 removed outlier: 3.657A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 847 through 856 removed outlier: 4.171A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 879 through 896 Processing helix chain 'B' and resid 912 through 921 Processing helix chain 'B' and resid 930 through 933 Processing helix chain 'B' and resid 941 through 944 No H-bonds generated for 'chain 'B' and resid 941 through 944' Processing helix chain 'B' and resid 951 through 953 No H-bonds generated for 'chain 'B' and resid 951 through 953' Processing helix chain 'B' and resid 956 through 961 Processing helix chain 'B' and resid 964 through 973 Processing helix chain 'B' and resid 977 through 990 Processing helix chain 'B' and resid 995 through 1003 Processing helix chain 'C' and resid 24 through 38 Processing helix chain 'C' and resid 48 through 53 removed outlier: 3.647A pdb=" N LEU C 53 " --> pdb=" O GLY C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 81 through 107 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 116 through 124 removed outlier: 3.559A pdb=" N MET C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 155 through 159 removed outlier: 4.459A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 159' Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 193 through 196 No H-bonds generated for 'chain 'C' and resid 193 through 196' Processing helix chain 'C' and resid 198 through 210 Processing helix chain 'C' and resid 223 through 234 removed outlier: 4.124A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 271 through 274 No H-bonds generated for 'chain 'C' and resid 271 through 274' Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'D' and resid 27 through 39 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 59 through 70 Processing helix chain 'D' and resid 81 through 94 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 116 through 124 removed outlier: 3.808A pdb=" N MET D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 193 through 196 No H-bonds generated for 'chain 'D' and resid 193 through 196' Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 223 through 234 Processing helix chain 'D' and resid 255 through 263 Processing helix chain 'D' and resid 271 through 274 No H-bonds generated for 'chain 'D' and resid 271 through 274' Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.617A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 76 Processing helix chain 'G' and resid 70 through 76 Processing sheet with id= A, first strand: chain 'A' and resid 212 through 216 removed outlier: 7.103A pdb=" N HIS A 128 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL A 46 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE A 130 " --> pdb=" O VAL A 46 " (cutoff:3.500A) 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) Processing sheet with id= B, first strand: chain 'A' and resid 243 through 247 removed outlier: 3.788A pdb=" N PHE A 245 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 338 through 340 Processing sheet with id= D, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.468A pdb=" N VAL B 129 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N THR B 212 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE B 45 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 214 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE B 244 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 338 through 340 Processing sheet with id= F, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.275A pdb=" N VAL C 129 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N THR C 212 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE C 45 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL C 214 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE C 244 " --> pdb=" O PHE C 215 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 212 through 216 removed outlier: 6.996A pdb=" N HIS D 128 " --> pdb=" O PHE D 44 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL D 46 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE D 130 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 243 through 247 Processing sheet with id= I, first strand: chain 'E' and resid 233 through 235 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) Processing sheet with id= J, first strand: chain 'E' and resid 198 through 201 removed outlier: 4.765A pdb=" N LYS E 219 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR E 29 " --> pdb=" O THR E 62 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 232 through 234 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: 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) 943 hydrogen bonds defined for protein. 2766 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.94 Time building geometry restraints manager: 9.42 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: 210 2.47 - 3.08: 16872 3.08 - 3.68: 34753 3.68 - 4.29: 54152 4.29 - 4.90: 90021 Nonbonded interactions: 196008 Sorted by model distance: nonbonded pdb=" OH TYR A 286 " pdb=" O2B NAD A1101 " model vdw 1.861 2.440 nonbonded pdb=" OE2 GLU B 685 " pdb=" OG SER B 729 " model vdw 1.997 2.440 nonbonded pdb=" OG SER D 51 " pdb=" OD2 ASP D 135 " model vdw 2.000 2.440 nonbonded pdb=" OH TYR A 414 " pdb=" OD1 ASN A 654 " model vdw 2.018 2.440 nonbonded pdb=" NH1 ARG D 247 " pdb=" OD1 ASP D 249 " model vdw 2.018 2.520 ... (remaining 196003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' 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: 7.990 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: 32.850 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 58.280 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.460 ------------------------------------------------------------------------------- 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= 0.337 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 : 2.557 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: 1.1185 time to fit residues: 660.5123 Evaluate side-chains 481 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 338 time to evaluate : 2.803 ------------------------------------------------------------------------------- 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: 0.6980 chunk 201 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 135 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 D 58 GLN D 67 HIS ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN E 197 ASN G 197 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0997 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= 0.291 Angle : 0.603 9.013 30904 Z= 0.310 Chirality : 0.043 0.189 3309 Planarity : 0.004 0.060 3916 Dihedral : 12.093 88.275 3402 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 8.64 % Allowed : 30.25 % Favored : 61.11 % 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: 0.33 (0.16), residues: 2624 helix: 0.99 (0.13), residues: 1540 sheet: -0.23 (0.43), residues: 122 loop : -0.90 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 60 HIS 0.006 0.001 HIS A 67 PHE 0.019 0.002 PHE A 500 TYR 0.019 0.002 TYR A 166 ARG 0.007 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 571 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 360 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.7582 (p0) cc_final: 0.7367 (p0) REVERT: A 254 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6281 (mp0) REVERT: A 316 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8424 (mp) REVERT: A 457 ASN cc_start: 0.8457 (t0) cc_final: 0.7908 (m110) REVERT: A 986 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: A 996 TYR cc_start: 0.7851 (m-80) cc_final: 0.7650 (m-80) REVERT: A 1003 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.4219 (p90) REVERT: B 25 ASN cc_start: 0.7409 (t0) cc_final: 0.6987 (t0) REVERT: B 64 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: B 98 MET cc_start: 0.7933 (mmm) cc_final: 0.7475 (mpp) REVERT: B 516 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: B 543 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7583 (tp30) REVERT: B 557 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8580 (mptt) REVERT: B 564 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8205 (mtmt) REVERT: B 982 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6932 (mt-10) REVERT: C 98 MET cc_start: 0.7154 (mmm) cc_final: 0.6259 (mmm) REVERT: C 280 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6813 (t80) REVERT: C 281 ASP cc_start: 0.6756 (m-30) cc_final: 0.6551 (p0) REVERT: D 54 SER cc_start: 0.6132 (OUTLIER) cc_final: 0.5786 (p) REVERT: D 185 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7504 (pp) REVERT: D 227 MET cc_start: 0.7983 (mmm) cc_final: 0.7767 (mmt) REVERT: D 247 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7005 (tmm160) REVERT: D 285 ARG cc_start: 0.7738 (ttp-110) cc_final: 0.7525 (ttp-110) REVERT: E 48 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6589 (ptmm) REVERT: G 14 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8179 (ptpp) REVERT: G 208 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7988 (pt) outliers start: 211 outliers final: 99 residues processed: 525 average time/residue: 1.1831 time to fit residues: 725.0103 Evaluate side-chains 439 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 324 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 186 LYS 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 277 SER 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 332 HIS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 399 ASP 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 695 ILE Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain A residue 1005 ILE 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 191 LEU Chi-restraints excluded: chain B residue 192 ASN 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 435 ASP 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 541 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 557 LYS 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 711 GLN Chi-restraints excluded: chain B residue 762 THR 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 847 THR Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 878 THR 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 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 115 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 194 ASP 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 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 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 8 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 48 LYS 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 8 THR 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 194 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 233 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: 0.6980 chunk 201 optimal weight: 0.3980 chunk 164 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 241 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 239 optimal weight: 0.0870 chunk 82 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN A 910 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN D 58 GLN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22897 Z= 0.192 Angle : 0.539 9.251 30904 Z= 0.279 Chirality : 0.040 0.215 3309 Planarity : 0.004 0.049 3916 Dihedral : 9.983 83.404 3281 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 7.20 % Allowed : 31.03 % Favored : 61.77 % 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: 0.33 (0.16), residues: 2624 helix: 0.99 (0.13), residues: 1537 sheet: -0.10 (0.44), residues: 121 loop : -0.93 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 60 HIS 0.008 0.001 HIS A 67 PHE 0.016 0.001 PHE E 23 TYR 0.023 0.001 TYR A 951 ARG 0.006 0.000 ARG E 170 *********************** 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 539 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 363 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.7571 (p0) cc_final: 0.7361 (p0) REVERT: A 316 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 457 ASN cc_start: 0.8354 (t0) cc_final: 0.7897 (m-40) REVERT: A 574 TYR cc_start: 0.8610 (m-80) cc_final: 0.8383 (m-80) REVERT: A 765 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8202 (p0) REVERT: A 875 ASP cc_start: 0.7565 (t0) cc_final: 0.7307 (m-30) REVERT: A 1003 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.4738 (p90) REVERT: B 25 ASN cc_start: 0.7342 (t0) cc_final: 0.6934 (t0) REVERT: B 64 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: B 98 MET cc_start: 0.7938 (mmm) cc_final: 0.7498 (mpp) REVERT: B 543 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8303 (tp30) REVERT: B 564 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8233 (mtmt) REVERT: C 98 MET cc_start: 0.7156 (mmm) cc_final: 0.6408 (mmm) REVERT: C 280 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6751 (t80) REVERT: C 281 ASP cc_start: 0.6611 (m-30) cc_final: 0.6315 (p0) REVERT: D 184 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8674 (m) REVERT: D 185 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7414 (pp) REVERT: D 227 MET cc_start: 0.7968 (mmm) cc_final: 0.7744 (mmt) REVERT: D 247 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6734 (tmm160) REVERT: D 253 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7768 (mt) REVERT: D 262 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: E 214 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5774 (mm) REVERT: G 15 ARG cc_start: 0.8125 (ttm110) cc_final: 0.7616 (ttm-80) REVERT: G 51 TYR cc_start: 0.7663 (t80) cc_final: 0.7166 (t80) REVERT: G 208 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7900 (pt) outliers start: 176 outliers final: 80 residues processed: 494 average time/residue: 1.1668 time to fit residues: 671.7052 Evaluate side-chains 411 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 317 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP 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 227 MET 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 399 ASP Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 603 VAL 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 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 1003 TYR 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 191 LEU Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 497 LEU 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 711 GLN 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 847 THR 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 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 941 ASP Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 139 ASP 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 64 ASP Chi-restraints excluded: chain D residue 79 TYR 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 184 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 192 ASN 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 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 8 THR 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 226 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 234 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 230 optimal weight: 0.0000 chunk 69 optimal weight: 0.2980 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN A 910 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 GLN B 927 ASN D 128 HIS D 236 GLN E 65 ASN G 65 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22897 Z= 0.247 Angle : 0.544 8.602 30904 Z= 0.284 Chirality : 0.041 0.187 3309 Planarity : 0.004 0.045 3916 Dihedral : 9.334 78.424 3235 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 7.70 % Allowed : 30.54 % Favored : 61.77 % 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: 0.87 (0.13), residues: 1533 sheet: -0.04 (0.45), residues: 121 loop : -0.93 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 60 HIS 0.006 0.001 HIS D 128 PHE 0.017 0.002 PHE G 67 TYR 0.025 0.001 TYR A 951 ARG 0.007 0.000 ARG B 61 *********************** 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 533 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 345 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: A 93 ASN cc_start: 0.7649 (p0) cc_final: 0.7411 (p0) REVERT: A 316 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8420 (mp) REVERT: A 374 SER cc_start: 0.5929 (OUTLIER) cc_final: 0.5647 (t) REVERT: A 433 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: A 457 ASN cc_start: 0.8413 (t0) cc_final: 0.7920 (m-40) REVERT: A 913 MET cc_start: 0.7333 (mtp) cc_final: 0.7051 (ttp) REVERT: A 1003 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.4895 (p90) REVERT: B 25 ASN cc_start: 0.7363 (t0) cc_final: 0.6952 (t0) REVERT: B 64 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: B 98 MET cc_start: 0.7973 (mmm) cc_final: 0.7561 (mpp) REVERT: B 543 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8345 (tp30) REVERT: C 98 MET cc_start: 0.7070 (mmm) cc_final: 0.6379 (mmm) REVERT: C 195 GLN cc_start: 0.8129 (pt0) cc_final: 0.7882 (tm-30) REVERT: C 280 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.6810 (t80) REVERT: C 281 ASP cc_start: 0.6594 (m-30) cc_final: 0.6304 (p0) REVERT: C 290 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.7051 (mmt) REVERT: D 98 MET cc_start: 0.7786 (tpp) cc_final: 0.7468 (tpt) REVERT: D 106 ASP cc_start: 0.7896 (m-30) cc_final: 0.7676 (m-30) REVERT: D 184 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8670 (m) REVERT: D 235 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7933 (mp) REVERT: D 247 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6711 (tmm160) REVERT: D 251 SER cc_start: 0.8000 (m) cc_final: 0.7759 (p) REVERT: D 253 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7732 (mt) REVERT: D 262 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: G 14 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8234 (ptpp) REVERT: G 15 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7669 (ttm-80) REVERT: G 208 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.7924 (pt) outliers start: 188 outliers final: 102 residues processed: 487 average time/residue: 1.1603 time to fit residues: 661.2842 Evaluate side-chains 442 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 324 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 134 TYR 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 179 LYS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 227 MET 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 399 ASP Chi-restraints excluded: chain A residue 433 GLU 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 750 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 862 ILE 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 1003 TYR 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 192 ASN 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 368 ASP Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 602 SER 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 711 GLN Chi-restraints excluded: chain B residue 731 GLU Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 847 THR 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 878 THR 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 938 ASP Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 192 ASN 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 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 8 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 14 LYS 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 194 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 234 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 0.5980 chunk 230 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 GLN B 927 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: 0.8265 moved from start: 0.1612 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= 0.287 Angle : 0.554 8.913 30904 Z= 0.288 Chirality : 0.042 0.186 3309 Planarity : 0.004 0.043 3916 Dihedral : 9.080 74.805 3224 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 8.27 % Allowed : 30.09 % Favored : 61.65 % 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: 0.11 (0.16), residues: 2624 helix: 0.78 (0.13), residues: 1529 sheet: -0.08 (0.45), residues: 121 loop : -0.97 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 60 HIS 0.003 0.001 HIS B 67 PHE 0.016 0.002 PHE A 500 TYR 0.025 0.001 TYR A 951 ARG 0.007 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 536 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 334 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: A 76 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8084 (tptp) REVERT: A 254 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6014 (mm-30) REVERT: A 316 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8395 (mp) REVERT: A 374 SER cc_start: 0.5979 (OUTLIER) cc_final: 0.5685 (t) REVERT: A 433 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: A 457 ASN cc_start: 0.8421 (t0) cc_final: 0.7947 (m-40) REVERT: B 25 ASN cc_start: 0.7386 (t0) cc_final: 0.6979 (t0) REVERT: B 64 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: B 98 MET cc_start: 0.7956 (mmm) cc_final: 0.7550 (mpp) REVERT: B 389 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: B 543 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8349 (tp30) REVERT: B 557 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8621 (mptt) REVERT: C 98 MET cc_start: 0.7019 (mmm) cc_final: 0.6342 (mmm) REVERT: C 175 ARG cc_start: 0.8550 (mtm110) cc_final: 0.8345 (mtm110) REVERT: C 195 GLN cc_start: 0.8136 (pt0) cc_final: 0.7897 (tm-30) REVERT: C 280 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6796 (t80) REVERT: C 281 ASP cc_start: 0.6541 (m-30) cc_final: 0.6311 (p0) REVERT: C 290 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.7058 (mmt) REVERT: D 98 MET cc_start: 0.7910 (tpp) cc_final: 0.7570 (tpt) REVERT: D 106 ASP cc_start: 0.7889 (m-30) cc_final: 0.7634 (m-30) REVERT: D 185 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7508 (pp) REVERT: D 235 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7932 (mp) REVERT: D 247 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6555 (tmm160) REVERT: D 253 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7677 (mt) REVERT: D 262 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: E 20 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7112 (tptt) REVERT: E 39 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: E 214 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5776 (mm) REVERT: G 14 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8241 (ptpp) REVERT: G 15 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7649 (ttm-80) REVERT: G 51 TYR cc_start: 0.7736 (t80) cc_final: 0.7220 (t80) REVERT: G 208 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8185 (pt) outliers start: 202 outliers final: 99 residues processed: 487 average time/residue: 1.1806 time to fit residues: 669.8021 Evaluate side-chains 443 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 322 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 167 LEU 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 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 399 ASP Chi-restraints excluded: chain A residue 433 GLU 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 750 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 1003 TYR 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 192 ASN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 602 SER 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 711 GLN Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 878 THR 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 938 ASP Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 280 TYR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 134 TYR 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 235 LEU 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 8 THR Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 193 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 8 THR Chi-restraints excluded: chain G residue 14 LYS 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 194 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 234 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 0.6980 chunk 231 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 119 optimal weight: 0.0030 chunk 21 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 332 HIS ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 GLN B 927 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN G 65 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 22897 Z= 0.192 Angle : 0.522 7.820 30904 Z= 0.273 Chirality : 0.040 0.182 3309 Planarity : 0.003 0.043 3916 Dihedral : 8.711 71.169 3214 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 6.92 % Allowed : 31.44 % Favored : 61.65 % 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: 0.23 (0.16), residues: 2624 helix: 0.89 (0.13), residues: 1525 sheet: -0.05 (0.46), residues: 121 loop : -0.92 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 60 HIS 0.003 0.001 HIS A 978 PHE 0.018 0.001 PHE G 67 TYR 0.023 0.001 TYR A 951 ARG 0.009 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 512 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 343 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: A 93 ASN cc_start: 0.7641 (p0) cc_final: 0.7414 (p0) REVERT: A 316 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8380 (mp) REVERT: A 374 SER cc_start: 0.5808 (OUTLIER) cc_final: 0.5553 (t) REVERT: A 433 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: A 457 ASN cc_start: 0.8352 (t0) cc_final: 0.7906 (m-40) REVERT: B 25 ASN cc_start: 0.7351 (t0) cc_final: 0.6961 (t0) REVERT: B 64 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: B 98 MET cc_start: 0.7964 (mmm) cc_final: 0.7579 (mpp) REVERT: B 339 HIS cc_start: 0.8132 (t-90) cc_final: 0.7871 (t-90) REVERT: B 543 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8332 (tp30) REVERT: B 557 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8630 (mptt) REVERT: C 98 MET cc_start: 0.6921 (mmm) cc_final: 0.6271 (mmm) REVERT: C 195 GLN cc_start: 0.8114 (pt0) cc_final: 0.7874 (tm-30) REVERT: C 280 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.6756 (t80) REVERT: C 281 ASP cc_start: 0.6504 (m-30) cc_final: 0.6212 (p0) REVERT: C 290 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.7031 (mmt) REVERT: D 106 ASP cc_start: 0.7928 (m-30) cc_final: 0.7664 (m-30) REVERT: D 124 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8657 (mmt) REVERT: D 185 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7454 (pp) REVERT: D 247 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6568 (tmm160) REVERT: D 253 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7715 (mt) REVERT: D 262 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: E 39 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: G 15 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7603 (ttm-80) REVERT: G 51 TYR cc_start: 0.7723 (t80) cc_final: 0.7228 (t80) REVERT: G 208 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8100 (pt) outliers start: 169 outliers final: 85 residues processed: 464 average time/residue: 1.2191 time to fit residues: 659.4119 Evaluate side-chains 418 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 317 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 216 ILE 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 433 GLU 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 524 ILE 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 750 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain B residue 58 GLN 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 191 LEU Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 602 SER 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 731 GLU Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 878 THR 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 941 ASP Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 192 ASN 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 110 VAL Chi-restraints excluded: chain D residue 124 MET 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 192 ASN 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 39 GLU Chi-restraints excluded: chain E residue 52 ILE 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 194 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 146 optimal weight: 0.9980 chunk 187 optimal weight: 0.0970 chunk 145 optimal weight: 0.5980 chunk 216 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 118 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 160 ASN A 332 HIS ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN A 910 ASN A 979 HIS ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 GLN B 927 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN E 194 GLN G 65 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 22897 Z= 0.217 Angle : 0.522 7.333 30904 Z= 0.275 Chirality : 0.040 0.182 3309 Planarity : 0.003 0.043 3916 Dihedral : 8.470 68.764 3204 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.75 % Allowed : 31.48 % Favored : 61.77 % 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: 0.21 (0.16), residues: 2624 helix: 0.86 (0.13), residues: 1527 sheet: -0.26 (0.45), residues: 131 loop : -0.89 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 60 HIS 0.005 0.001 HIS A 979 PHE 0.023 0.001 PHE B 576 TYR 0.021 0.001 TYR A 951 ARG 0.008 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 498 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 333 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8087 (tptp) REVERT: A 93 ASN cc_start: 0.7548 (p0) cc_final: 0.7334 (p0) REVERT: A 316 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8356 (mp) REVERT: A 374 SER cc_start: 0.5780 (OUTLIER) cc_final: 0.5517 (t) REVERT: A 433 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: A 457 ASN cc_start: 0.8351 (t0) cc_final: 0.7923 (m-40) REVERT: B 25 ASN cc_start: 0.7350 (t0) cc_final: 0.6951 (t0) REVERT: B 64 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: B 98 MET cc_start: 0.7849 (mmm) cc_final: 0.7360 (mpp) REVERT: B 339 HIS cc_start: 0.8197 (t-90) cc_final: 0.7957 (t-90) REVERT: B 389 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: B 543 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: B 557 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8633 (mptt) REVERT: C 98 MET cc_start: 0.6913 (mmm) cc_final: 0.6301 (mmm) REVERT: C 195 GLN cc_start: 0.8111 (pt0) cc_final: 0.7885 (tm-30) REVERT: C 280 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6751 (t80) REVERT: C 281 ASP cc_start: 0.6468 (m-30) cc_final: 0.6160 (p0) REVERT: C 290 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6972 (mmt) REVERT: D 106 ASP cc_start: 0.7944 (m-30) cc_final: 0.7632 (m-30) REVERT: D 124 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8684 (mmt) REVERT: D 185 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7543 (pp) REVERT: D 235 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7835 (mp) REVERT: D 247 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6540 (tmm160) REVERT: D 253 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7555 (mt) REVERT: D 262 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: E 20 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7011 (tptm) REVERT: E 39 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: E 214 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5687 (mm) REVERT: G 14 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8229 (ptpp) REVERT: G 15 ARG cc_start: 0.8126 (ttm110) cc_final: 0.7631 (ttm-80) REVERT: G 51 TYR cc_start: 0.7796 (t80) cc_final: 0.7244 (t80) REVERT: G 208 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8104 (pt) outliers start: 165 outliers final: 92 residues processed: 458 average time/residue: 1.2144 time to fit residues: 645.8697 Evaluate side-chains 428 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 315 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 216 ILE 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 433 GLU 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 738 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 951 TYR Chi-restraints excluded: chain A residue 1003 TYR 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 192 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 695 ILE 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 770 SER 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 862 ILE Chi-restraints excluded: chain B residue 878 THR 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 941 ASP Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 192 ASN 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 79 TYR Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 124 MET 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 192 ASN 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 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 20 LYS Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 52 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 230 GLU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 58 GLU 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 Chi-restraints excluded: chain G residue 234 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 153 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN A 910 ASN A 979 HIS ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 GLN B 927 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN G 65 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22897 Z= 0.222 Angle : 0.537 12.112 30904 Z= 0.281 Chirality : 0.040 0.182 3309 Planarity : 0.003 0.042 3916 Dihedral : 8.271 69.400 3197 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.10 % Allowed : 32.21 % Favored : 61.69 % 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: 0.19 (0.16), residues: 2624 helix: 0.85 (0.13), residues: 1524 sheet: -0.23 (0.45), residues: 131 loop : -0.91 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 60 HIS 0.007 0.001 HIS A 979 PHE 0.021 0.001 PHE B 576 TYR 0.022 0.001 TYR A 951 ARG 0.009 0.000 ARG D 233 *********************** 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 481 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 332 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: A 76 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8086 (tptp) REVERT: A 93 ASN cc_start: 0.7550 (p0) cc_final: 0.7333 (p0) REVERT: A 316 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 374 SER cc_start: 0.5786 (OUTLIER) cc_final: 0.5516 (t) REVERT: A 433 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: A 457 ASN cc_start: 0.8349 (t0) cc_final: 0.7931 (m-40) REVERT: B 25 ASN cc_start: 0.7342 (t0) cc_final: 0.6950 (t0) REVERT: B 98 MET cc_start: 0.7867 (mmm) cc_final: 0.7477 (mpp) REVERT: B 339 HIS cc_start: 0.8228 (t-90) cc_final: 0.7971 (t-90) REVERT: B 389 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: B 543 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: B 557 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8630 (mptt) REVERT: C 98 MET cc_start: 0.6904 (mmm) cc_final: 0.6303 (mmm) REVERT: C 195 GLN cc_start: 0.8105 (pt0) cc_final: 0.7886 (tm-30) REVERT: C 280 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6765 (t80) REVERT: C 281 ASP cc_start: 0.6472 (m-30) cc_final: 0.6167 (p0) REVERT: C 290 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6954 (mmt) REVERT: D 106 ASP cc_start: 0.7894 (m-30) cc_final: 0.7541 (m-30) REVERT: D 124 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8709 (mmt) REVERT: D 185 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7544 (pp) REVERT: D 247 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6502 (tmm160) REVERT: D 253 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7640 (mt) REVERT: D 262 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: E 20 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7018 (tptm) REVERT: E 39 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: E 214 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5706 (mm) REVERT: G 15 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7608 (ttm-80) REVERT: G 51 TYR cc_start: 0.7782 (t80) cc_final: 0.7230 (t80) REVERT: G 208 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8116 (pt) outliers start: 149 outliers final: 96 residues processed: 444 average time/residue: 1.2064 time to fit residues: 627.3398 Evaluate side-chains 429 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 314 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 228 LEU 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 433 GLU 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 750 ASP Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 951 TYR Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 707 VAL 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 770 SER 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 862 ILE Chi-restraints excluded: chain B residue 878 THR 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 941 ASP Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 192 ASN 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 79 TYR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 124 MET 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 192 ASN 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 20 LYS Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 52 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 194 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 234 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.8980 chunk 245 optimal weight: 0.6980 chunk 224 optimal weight: 3.9990 chunk 238 optimal weight: 0.6980 chunk 143 optimal weight: 0.0670 chunk 104 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 263 ASN A 332 HIS ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN A 979 HIS ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN G 65 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22897 Z= 0.206 Angle : 0.537 9.464 30904 Z= 0.283 Chirality : 0.040 0.181 3309 Planarity : 0.003 0.042 3916 Dihedral : 8.106 71.410 3197 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.57 % Allowed : 33.07 % Favored : 61.36 % 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: 0.21 (0.16), residues: 2624 helix: 0.87 (0.13), residues: 1524 sheet: -0.15 (0.46), residues: 131 loop : -0.92 (0.18), residues: 969 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 0.020 0.001 PHE B 576 TYR 0.020 0.001 TYR A 951 ARG 0.008 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 465 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 329 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: A 76 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8065 (tptp) REVERT: A 93 ASN cc_start: 0.7516 (p0) cc_final: 0.7286 (p0) REVERT: A 98 MET cc_start: 0.8081 (mpp) cc_final: 0.7748 (mpp) REVERT: A 316 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8339 (mp) REVERT: A 374 SER cc_start: 0.5711 (OUTLIER) cc_final: 0.5466 (t) REVERT: A 433 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: A 435 ASP cc_start: 0.8133 (t70) cc_final: 0.7499 (m-30) REVERT: A 457 ASN cc_start: 0.8335 (t0) cc_final: 0.7950 (m-40) REVERT: B 25 ASN cc_start: 0.7331 (t0) cc_final: 0.6942 (t0) REVERT: B 98 MET cc_start: 0.7861 (mmm) cc_final: 0.7470 (mpp) REVERT: B 339 HIS cc_start: 0.8212 (t-90) cc_final: 0.8000 (t-90) REVERT: B 389 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: B 543 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8309 (tp30) REVERT: B 557 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8621 (mptt) REVERT: B 568 GLU cc_start: 0.8143 (mp0) cc_final: 0.7922 (mp0) REVERT: C 98 MET cc_start: 0.6893 (mmm) cc_final: 0.6323 (mmm) REVERT: C 280 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6790 (t80) REVERT: C 281 ASP cc_start: 0.6448 (m-30) cc_final: 0.6146 (p0) REVERT: C 290 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6842 (mmt) REVERT: D 106 ASP cc_start: 0.7844 (m-30) cc_final: 0.7477 (m-30) REVERT: D 124 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8688 (mmt) REVERT: D 185 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7510 (pp) REVERT: D 233 ARG cc_start: 0.8308 (ppp80) cc_final: 0.7819 (ptt90) REVERT: D 247 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6575 (tmm160) REVERT: D 253 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7647 (mt) REVERT: D 262 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: E 20 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.6992 (tptm) REVERT: E 39 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: E 214 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5672 (mm) REVERT: G 15 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7580 (ttm-80) REVERT: G 51 TYR cc_start: 0.7752 (t80) cc_final: 0.7228 (t80) REVERT: G 208 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8091 (pt) outliers start: 136 outliers final: 94 residues processed: 432 average time/residue: 1.2178 time to fit residues: 612.1676 Evaluate side-chains 425 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 312 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 167 LEU 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 228 LEU 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 433 GLU 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 750 ASP Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 951 TYR Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 707 VAL 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 770 SER 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 862 ILE Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 904 ILE 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 941 ASP Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 139 ASP 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 79 TYR Chi-restraints excluded: chain D residue 124 MET 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 262 GLU 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 20 LYS Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 52 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 194 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 226 THR Chi-restraints excluded: chain G residue 233 VAL 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: 0.8980 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 211 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 167 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN A 910 ASN A 979 HIS ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN G 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 22897 Z= 0.224 Angle : 0.552 11.070 30904 Z= 0.290 Chirality : 0.041 0.182 3309 Planarity : 0.004 0.043 3916 Dihedral : 7.913 72.275 3192 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.49 % Allowed : 33.07 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2624 helix: 0.82 (0.13), residues: 1525 sheet: -0.15 (0.46), residues: 131 loop : -0.91 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 60 HIS 0.008 0.001 HIS A 979 PHE 0.019 0.001 PHE B 576 TYR 0.020 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 456 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 322 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: A 76 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8046 (tptp) REVERT: A 93 ASN cc_start: 0.7533 (p0) cc_final: 0.7317 (p0) REVERT: A 98 MET cc_start: 0.8084 (mpp) cc_final: 0.7757 (mpp) REVERT: A 316 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8348 (mp) REVERT: A 374 SER cc_start: 0.5687 (OUTLIER) cc_final: 0.5445 (t) REVERT: A 433 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: A 435 ASP cc_start: 0.8168 (t70) cc_final: 0.7540 (m-30) REVERT: A 457 ASN cc_start: 0.8337 (t0) cc_final: 0.7956 (m-40) REVERT: A 822 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: B 25 ASN cc_start: 0.7323 (t0) cc_final: 0.6937 (t0) REVERT: B 64 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: B 98 MET cc_start: 0.7853 (mmm) cc_final: 0.7466 (mpp) REVERT: B 339 HIS cc_start: 0.8219 (t-90) cc_final: 0.7992 (t-90) REVERT: B 389 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: B 434 ASP cc_start: 0.7952 (t0) cc_final: 0.7590 (m-30) REVERT: B 543 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8321 (tp30) REVERT: B 557 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8636 (mptt) REVERT: B 568 GLU cc_start: 0.8131 (mp0) cc_final: 0.7915 (mp0) REVERT: B 982 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7049 (mt-10) REVERT: C 98 MET cc_start: 0.6853 (mmm) cc_final: 0.6263 (mmm) REVERT: C 280 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6774 (t80) REVERT: C 281 ASP cc_start: 0.6412 (m-30) cc_final: 0.6142 (p0) REVERT: C 290 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6810 (mmt) REVERT: D 106 ASP cc_start: 0.7724 (m-30) cc_final: 0.7368 (m-30) REVERT: D 124 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8674 (mmt) REVERT: D 185 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7547 (pp) REVERT: D 233 ARG cc_start: 0.8298 (ppp80) cc_final: 0.7843 (ptt90) REVERT: D 247 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6579 (tmm160) REVERT: D 253 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7672 (mt) REVERT: D 262 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: E 20 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7000 (tptm) REVERT: E 39 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: E 214 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5651 (mm) REVERT: G 15 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7591 (ttm-80) REVERT: G 51 TYR cc_start: 0.7738 (t80) cc_final: 0.7199 (t80) REVERT: G 208 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8120 (pt) outliers start: 134 outliers final: 93 residues processed: 423 average time/residue: 1.2717 time to fit residues: 638.7878 Evaluate side-chains 417 residues out of total 2443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 303 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 167 LEU 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 228 LEU 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 399 ASP Chi-restraints excluded: chain A residue 433 GLU 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 750 ASP Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 951 TYR Chi-restraints excluded: chain A residue 1003 TYR 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 192 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 602 SER 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 707 VAL 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 770 SER 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 862 ILE Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 904 ILE 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 941 ASP Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 192 ASN 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 111 ASP Chi-restraints excluded: chain D residue 124 MET 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 262 GLU 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 20 LYS Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 52 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 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 226 THR Chi-restraints excluded: chain G residue 233 VAL 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: 0.0570 chunk 64 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 211 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 185 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN A 910 ASN A 979 HIS ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN G 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.167568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133883 restraints weight = 25666.314| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.10 r_work: 0.3233 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22897 Z= 0.205 Angle : 0.547 10.587 30904 Z= 0.286 Chirality : 0.040 0.181 3309 Planarity : 0.003 0.046 3916 Dihedral : 7.731 73.906 3190 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.99 % Allowed : 33.61 % Favored : 61.40 % 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: 0.21 (0.16), residues: 2624 helix: 0.85 (0.13), residues: 1525 sheet: -0.13 (0.46), residues: 131 loop : -0.90 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 60 HIS 0.008 0.001 HIS A 979 PHE 0.032 0.001 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: 9839.07 seconds wall clock time: 177 minutes 37.72 seconds (10657.72 seconds total)