Starting phenix.real_space_refine on Sun May 12 09:52:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyf_37926/05_2024/8wyf_37926_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyf_37926/05_2024/8wyf_37926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyf_37926/05_2024/8wyf_37926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyf_37926/05_2024/8wyf_37926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyf_37926/05_2024/8wyf_37926_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyf_37926/05_2024/8wyf_37926_neut_updated.pdb" } resolution = 2.85 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= 0.077 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 78 5.16 5 C 13832 2.51 5 N 3460 2.21 5 O 4030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 923": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B GLU 887": "OE1" <-> "OE2" Residue "B GLU 923": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 21408 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 945, 7895 Classifications: {'peptide': 945} Link IDs: {'PTRANS': 19, 'TRANS': 925} Chain breaks: 5 Chain: "B" Number of atoms: 7966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7966 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 19, 'TRANS': 933} Chain breaks: 6 Chain: "C" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2219 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Chain: "D" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2195 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Chain: "E" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 957 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} 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: 10.49, per 1000 atoms: 0.49 Number of scatterers: 21408 At special positions: 0 Unit cell: (99.24, 126.531, 180.286, 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 78 16.00 P 8 15.00 O 4030 8.00 N 3460 7.00 C 13832 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: 8.38 Conformation dependent library (CDL) restraints added in 3.6 seconds 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 143 helices and 9 sheets defined 59.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.58 Creating SS restraints... Processing helix chain 'A' and resid 24 through 39 Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.591A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 70 Processing helix chain 'A' and resid 81 through 108 removed outlier: 3.911A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 6.771A pdb=" N GLU A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N MET A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 156 through 159 No H-bonds generated for 'chain 'A' and resid 156 through 159' 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: 3.779A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 262 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 295 removed outlier: 3.658A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 321 Proline residue: A 318 - end of helix removed outlier: 4.461A pdb=" N ALA A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 removed outlier: 4.089A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 333' Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.836A pdb=" N SER A 371 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 418 through 426 Processing helix chain 'A' and resid 432 through 445 Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 469 through 494 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.512A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 571 removed outlier: 4.918A pdb=" N ASP A 553 " --> pdb=" O PHE A 550 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 554 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 597 Processing helix chain 'A' and resid 601 through 604 Processing helix chain 'A' and resid 606 through 628 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 661 through 670 Processing helix chain 'A' and resid 673 through 675 No H-bonds generated for 'chain 'A' and resid 673 through 675' Processing helix chain 'A' and resid 681 through 698 Processing helix chain 'A' and resid 706 through 725 removed outlier: 3.641A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR A 725 " --> pdb=" O TYR A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 741 Processing helix chain 'A' and resid 751 through 764 removed outlier: 4.456A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 787 Processing helix chain 'A' and resid 801 through 811 Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 833 through 840 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 847 through 856 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 922 Processing helix chain 'A' and resid 930 through 933 Processing helix chain 'A' and resid 938 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 961 Processing helix chain 'A' and resid 964 through 973 Processing helix chain 'A' and resid 977 through 990 Processing helix chain 'A' and resid 994 through 1003 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 24 through 39 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.709A 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 94 removed outlier: 3.757A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 116 through 124 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.360A 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 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' 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: 3.725A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 263 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 282 through 297 Processing helix chain 'B' and resid 305 through 321 Proline residue: B 318 - end of helix removed outlier: 4.437A pdb=" N ALA B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 334 removed outlier: 3.856A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 365 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.087A pdb=" N LYS B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 Processing helix chain 'B' and resid 418 through 426 Processing helix chain 'B' and resid 432 through 444 Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 469 through 494 Processing helix chain 'B' and resid 509 through 518 Processing helix chain 'B' and resid 526 through 529 No H-bonds generated for 'chain 'B' and resid 526 through 529' Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 540 through 546 removed outlier: 4.341A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 562 removed outlier: 3.604A pdb=" N LEU B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE B 559 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU B 560 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU B 561 " --> pdb=" O LYS B 557 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) 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 634 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 699 Processing helix chain 'B' and resid 706 through 725 removed outlier: 3.645A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 5.418A 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 762 removed outlier: 3.506A pdb=" N LEU B 761 " --> pdb=" O TRP B 757 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 762 " --> pdb=" O LEU B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 786 removed outlier: 3.525A pdb=" N HIS B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 811 Processing helix chain 'B' and resid 818 through 825 Processing helix chain 'B' and resid 832 through 840 removed outlier: 3.859A 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: 4.326A 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 913 through 921 Processing helix chain 'B' and resid 930 through 933 Processing helix chain 'B' and resid 938 through 944 Processing helix chain 'B' and resid 956 through 960 Processing helix chain 'B' and resid 964 through 973 Processing helix chain 'B' and resid 977 through 991 Processing helix chain 'B' and resid 994 through 1002 Processing helix chain 'C' and resid 24 through 39 Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 81 through 94 removed outlier: 3.749A pdb=" N LEU C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 116 through 123 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.935A 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 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' 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: 3.637A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 263 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 296 removed outlier: 3.955A pdb=" N LEU C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 59 through 71 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: 3.914A pdb=" N MET D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 156 through 160 removed outlier: 3.704A pdb=" N ASN D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 156 through 160' Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' 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 removed outlier: 3.780A pdb=" N LYS D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 96 through 106 Processing sheet with id= A, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.506A pdb=" N VAL A 129 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N THR A 212 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE A 45 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A 214 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE A 244 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 338 through 340 Processing sheet with id= C, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.873A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N THR B 212 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE B 45 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL B 214 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE B 244 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 338 through 340 Processing sheet with id= E, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.278A pdb=" N VAL C 129 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ILE C 130 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE C 44 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR C 212 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE C 45 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL C 214 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE C 244 " --> pdb=" O PHE C 215 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.847A pdb=" N LEU D 42 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ILE D 130 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR D 212 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE D 45 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 214 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE D 244 " --> pdb=" O PHE D 215 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 15 through 17 Processing sheet with id= H, first strand: chain 'E' and resid 62 through 68 removed outlier: 6.070A pdb=" N GLU E 115 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE E 48 " --> pdb=" O GLU E 115 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL E 117 " --> pdb=" O PHE E 48 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 27 through 33 removed outlier: 6.596A pdb=" N VAL E 32 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE E 83 " --> pdb=" O VAL E 32 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.01 Time building geometry restraints manager: 9.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3739 1.32 - 1.44: 6037 1.44 - 1.57: 12003 1.57 - 1.69: 15 1.69 - 1.81: 129 Bond restraints: 21923 Sorted by residual: bond pdb=" O3 NAD A1101 " pdb=" PA NAD A1101 " ideal model delta sigma weight residual 1.653 1.566 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" O3 NAD C1101 " pdb=" PA NAD C1101 " ideal model delta sigma weight residual 1.653 1.581 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C4A NAD D1101 " pdb=" N9A NAD D1101 " ideal model delta sigma weight residual 1.367 1.303 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O5B NAD A1101 " pdb=" PA NAD A1101 " ideal model delta sigma weight residual 1.638 1.574 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C5A NAD D1101 " pdb=" C6A NAD D1101 " ideal model delta sigma weight residual 1.407 1.468 -0.061 2.00e-02 2.50e+03 9.18e+00 ... (remaining 21918 not shown) Histogram of bond angle deviations from ideal: 93.48 - 102.08: 61 102.08 - 110.67: 6533 110.67 - 119.26: 11237 119.26 - 127.85: 11617 127.85 - 136.44: 162 Bond angle restraints: 29610 Sorted by residual: angle pdb=" C2B NAD D1101 " pdb=" C1B NAD D1101 " pdb=" N9A NAD D1101 " ideal model delta sigma weight residual 114.24 99.64 14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CA GLN C 109 " pdb=" CB GLN C 109 " pdb=" CG GLN C 109 " ideal model delta sigma weight residual 114.10 122.57 -8.47 2.00e+00 2.50e-01 1.80e+01 angle pdb=" C1B NAD A1101 " pdb=" C2B NAD A1101 " pdb=" O2B NAD A1101 " ideal model delta sigma weight residual 113.98 102.88 11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C2A NAD A1101 " pdb=" N3A NAD A1101 " pdb=" C4A NAD A1101 " ideal model delta sigma weight residual 111.69 122.68 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C2A NAD B1101 " pdb=" N3A NAD B1101 " pdb=" C4A NAD B1101 " ideal model delta sigma weight residual 111.69 122.10 -10.41 3.00e+00 1.11e-01 1.20e+01 ... (remaining 29605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.23: 10912 18.23 - 36.47: 1666 36.47 - 54.70: 429 54.70 - 72.94: 83 72.94 - 91.17: 48 Dihedral angle restraints: 13138 sinusoidal: 5561 harmonic: 7577 Sorted by residual: dihedral pdb=" CA TYR C 166 " pdb=" C TYR C 166 " pdb=" N LEU C 167 " pdb=" CA LEU C 167 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ILE E 20 " pdb=" C ILE E 20 " pdb=" N ASN E 21 " pdb=" CA ASN E 21 " ideal model delta harmonic sigma weight residual -180.00 -162.93 -17.07 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CG ARG A 165 " pdb=" CD ARG A 165 " pdb=" NE ARG A 165 " pdb=" CZ ARG A 165 " ideal model delta sinusoidal sigma weight residual 90.00 43.22 46.78 2 1.50e+01 4.44e-03 1.13e+01 ... (remaining 13135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2955 0.073 - 0.146: 196 0.146 - 0.219: 6 0.219 - 0.292: 5 0.292 - 0.365: 2 Chirality restraints: 3164 Sorted by residual: chirality pdb=" C4D NAD D1101 " pdb=" C3D NAD D1101 " pdb=" C5D NAD D1101 " pdb=" O4D NAD D1101 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.36 2.00e-01 2.50e+01 3.33e+00 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 -2.40 -0.32 2.00e-01 2.50e+01 2.49e+00 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 -2.42 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 3161 not shown) Planarity restraints: 3744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 109 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C GLN C 109 " -0.047 2.00e-02 2.50e+03 pdb=" O GLN C 109 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 110 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B NAD B1101 " -0.025 2.00e-02 2.50e+03 1.15e-02 3.62e+00 pdb=" C2A NAD B1101 " 0.009 2.00e-02 2.50e+03 pdb=" C4A NAD B1101 " 0.004 2.00e-02 2.50e+03 pdb=" C5A NAD B1101 " -0.011 2.00e-02 2.50e+03 pdb=" C6A NAD B1101 " -0.010 2.00e-02 2.50e+03 pdb=" C8A NAD B1101 " 0.015 2.00e-02 2.50e+03 pdb=" N1A NAD B1101 " -0.004 2.00e-02 2.50e+03 pdb=" N3A NAD B1101 " 0.008 2.00e-02 2.50e+03 pdb=" N6A NAD B1101 " -0.002 2.00e-02 2.50e+03 pdb=" N7A NAD B1101 " 0.003 2.00e-02 2.50e+03 pdb=" N9A NAD B1101 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 559 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C PHE A 559 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE A 559 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU A 560 " -0.010 2.00e-02 2.50e+03 ... (remaining 3741 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 269 2.54 - 3.13: 17969 3.13 - 3.72: 35620 3.72 - 4.31: 51843 4.31 - 4.90: 84419 Nonbonded interactions: 190120 Sorted by model distance: nonbonded pdb=" OG SER B 37 " pdb=" O MET B 124 " model vdw 1.949 2.440 nonbonded pdb=" OE2 GLU A 685 " pdb=" OG SER A 729 " model vdw 1.972 2.440 nonbonded pdb=" OH TYR B 286 " pdb=" O2B NAD B1101 " model vdw 1.994 2.440 nonbonded pdb=" OH TYR A 324 " pdb=" OD1 ASP A 590 " model vdw 1.999 2.440 nonbonded pdb=" OH TYR B 472 " pdb=" OG SER B 546 " model vdw 2.018 2.440 ... (remaining 190115 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 22 through 496 or resid 502 through 565 or resid 579 throu \ gh 1005 or resid 1101)) selection = (chain 'B' and (resid 22 through 462 or resid 468 through 629 or resid 645 throu \ gh 700 or resid 703 through 1005 or resid 1101)) } ncs_group { reference = (chain 'C' and (resid 26 through 297 or resid 1101)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 34.210 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 58.220 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.120 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:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.004 0.087 21923 Z= 0.251 Angle : 0.551 14.597 29610 Z= 0.257 Chirality : 0.040 0.365 3164 Planarity : 0.002 0.032 3744 Dihedral : 18.783 91.170 8264 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 35.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.37 % Allowed : 29.08 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.17), residues: 2517 helix: 1.62 (0.14), residues: 1520 sheet: -1.10 (0.52), residues: 78 loop : -0.08 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 60 HIS 0.009 0.001 HIS B 349 PHE 0.009 0.001 PHE B 699 TYR 0.017 0.001 TYR B 940 ARG 0.003 0.000 ARG A 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 262 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 517 ARG cc_start: 0.8455 (ttp-110) cc_final: 0.7813 (mtm110) REVERT: B 504 TYR cc_start: 0.5719 (OUTLIER) cc_final: 0.5099 (t80) REVERT: D 237 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8419 (mppt) REVERT: E 28 GLU cc_start: 0.7812 (mp0) cc_final: 0.7222 (mt-10) outliers start: 79 outliers final: 72 residues processed: 331 average time/residue: 1.1446 time to fit residues: 444.6327 Evaluate side-chains 331 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 258 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 0.0970 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 229 optimal weight: 4.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 797 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21923 Z= 0.202 Angle : 0.525 9.308 29610 Z= 0.268 Chirality : 0.040 0.233 3164 Planarity : 0.003 0.040 3744 Dihedral : 10.130 87.115 3145 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.05 % Allowed : 25.33 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2517 helix: 1.38 (0.14), residues: 1511 sheet: -0.99 (0.53), residues: 78 loop : -0.05 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 60 HIS 0.009 0.001 HIS B 349 PHE 0.021 0.001 PHE B 916 TYR 0.019 0.001 TYR B 951 ARG 0.005 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 284 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7443 (mtt90) cc_final: 0.7000 (mpp-170) REVERT: A 62 LEU cc_start: 0.8044 (mm) cc_final: 0.7730 (mm) REVERT: A 134 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.6867 (m-80) REVERT: A 370 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6632 (mmt90) REVERT: A 436 TYR cc_start: 0.8098 (t80) cc_final: 0.7822 (t80) REVERT: A 517 ARG cc_start: 0.8454 (ttp-110) cc_final: 0.7908 (mtm110) REVERT: A 674 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7879 (t70) REVERT: A 787 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6171 (tt) REVERT: A 844 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7486 (mp) REVERT: A 856 PHE cc_start: 0.5476 (OUTLIER) cc_final: 0.4607 (t80) REVERT: A 945 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7479 (p0) REVERT: A 961 ASN cc_start: 0.8363 (m110) cc_final: 0.8109 (m110) REVERT: B 54 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.8121 (m) REVERT: B 69 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: B 107 PHE cc_start: 0.7582 (m-80) cc_final: 0.7270 (m-80) REVERT: B 222 ASP cc_start: 0.8188 (t0) cc_final: 0.7977 (t0) REVERT: B 504 TYR cc_start: 0.5751 (OUTLIER) cc_final: 0.5051 (t80) REVERT: B 521 ASN cc_start: 0.7650 (t0) cc_final: 0.6996 (t0) REVERT: B 936 MET cc_start: 0.3657 (pmm) cc_final: 0.3384 (pmm) REVERT: C 84 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: C 269 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7176 (pt) REVERT: D 107 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6010 (t80) REVERT: D 124 MET cc_start: 0.7552 (mmm) cc_final: 0.7211 (mmm) REVERT: D 134 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.7074 (p90) REVERT: D 237 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8410 (mppt) REVERT: E 26 ASP cc_start: 0.8315 (t0) cc_final: 0.8109 (t0) REVERT: E 28 GLU cc_start: 0.7955 (mp0) cc_final: 0.7390 (mt-10) REVERT: E 37 LYS cc_start: 0.7503 (tptm) cc_final: 0.7048 (ttpt) outliers start: 95 outliers final: 29 residues processed: 350 average time/residue: 1.1875 time to fit residues: 484.1847 Evaluate side-chains 293 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 250 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 856 PHE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 975 HIS Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain E residue 108 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 228 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 765 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21923 Z= 0.194 Angle : 0.492 8.526 29610 Z= 0.254 Chirality : 0.039 0.228 3164 Planarity : 0.003 0.041 3744 Dihedral : 8.804 89.607 3061 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.05 % Allowed : 26.48 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.16), residues: 2517 helix: 1.28 (0.13), residues: 1521 sheet: -0.58 (0.58), residues: 68 loop : -0.09 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 60 HIS 0.010 0.001 HIS B 349 PHE 0.013 0.001 PHE B 699 TYR 0.012 0.001 TYR B 951 ARG 0.004 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 279 time to evaluate : 2.603 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8032 (mm) cc_final: 0.7733 (mm) REVERT: A 134 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: A 386 ASN cc_start: 0.7953 (m110) cc_final: 0.7709 (m110) REVERT: A 436 TYR cc_start: 0.8155 (t80) cc_final: 0.7843 (t80) REVERT: A 517 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.7915 (mtm110) REVERT: A 674 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7894 (t70) REVERT: A 784 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7126 (mp0) REVERT: A 787 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.6221 (tt) REVERT: A 844 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7465 (mp) REVERT: A 856 PHE cc_start: 0.5502 (OUTLIER) cc_final: 0.4636 (t80) REVERT: A 961 ASN cc_start: 0.8421 (m110) cc_final: 0.8192 (m110) REVERT: A 974 LYS cc_start: 0.7884 (pptt) cc_final: 0.7265 (pmmt) REVERT: B 17 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6590 (tp30) REVERT: B 54 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.8105 (m) REVERT: B 69 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: B 222 ASP cc_start: 0.8129 (t0) cc_final: 0.7917 (t0) REVERT: B 504 TYR cc_start: 0.5753 (OUTLIER) cc_final: 0.5054 (t80) REVERT: B 521 ASN cc_start: 0.7669 (t0) cc_final: 0.6958 (t0) REVERT: B 758 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8975 (tp) REVERT: B 936 MET cc_start: 0.3679 (pmm) cc_final: 0.3325 (pmm) REVERT: C 84 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7295 (m-10) REVERT: C 119 ASP cc_start: 0.7653 (m-30) cc_final: 0.6890 (p0) REVERT: C 269 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7138 (pt) REVERT: D 61 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7248 (mmp-170) REVERT: D 107 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.5972 (t80) REVERT: D 134 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7213 (p90) REVERT: D 237 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8421 (mppt) REVERT: D 274 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7698 (tt) REVERT: E 26 ASP cc_start: 0.8322 (t0) cc_final: 0.8042 (t0) REVERT: E 37 LYS cc_start: 0.7481 (tptm) cc_final: 0.7037 (ttpt) outliers start: 95 outliers final: 34 residues processed: 345 average time/residue: 1.1648 time to fit residues: 468.0018 Evaluate side-chains 312 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 263 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 856 PHE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 975 HIS Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS B 797 ASN D 58 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21923 Z= 0.260 Angle : 0.512 8.258 29610 Z= 0.265 Chirality : 0.040 0.224 3164 Planarity : 0.003 0.044 3744 Dihedral : 8.477 89.881 3051 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.22 % Allowed : 26.65 % Favored : 69.13 % 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: 0.89 (0.16), residues: 2517 helix: 1.15 (0.13), residues: 1521 sheet: -0.52 (0.56), residues: 75 loop : -0.12 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 60 HIS 0.011 0.001 HIS B 349 PHE 0.024 0.001 PHE C 244 TYR 0.016 0.001 TYR B 951 ARG 0.005 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 277 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7688 (mtt90) cc_final: 0.7103 (mpp-170) REVERT: A 62 LEU cc_start: 0.8043 (mm) cc_final: 0.7729 (mm) REVERT: A 134 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.6268 (m-80) REVERT: A 386 ASN cc_start: 0.7996 (m110) cc_final: 0.7747 (m110) REVERT: A 436 TYR cc_start: 0.8380 (t80) cc_final: 0.8086 (t80) REVERT: A 517 ARG cc_start: 0.8516 (ttp-110) cc_final: 0.7917 (mtm110) REVERT: A 674 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7903 (t70) REVERT: A 784 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7096 (mp0) REVERT: A 787 ILE cc_start: 0.6474 (OUTLIER) cc_final: 0.6204 (tt) REVERT: A 844 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7476 (mp) REVERT: A 856 PHE cc_start: 0.5497 (OUTLIER) cc_final: 0.4800 (t80) REVERT: A 961 ASN cc_start: 0.8445 (m110) cc_final: 0.8225 (m110) REVERT: A 974 LYS cc_start: 0.7927 (pptt) cc_final: 0.7286 (pmmt) REVERT: B 17 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6663 (tp30) REVERT: B 54 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8192 (m) REVERT: B 65 LYS cc_start: 0.8019 (mmtp) cc_final: 0.7810 (mmtp) REVERT: B 69 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: B 222 ASP cc_start: 0.8186 (t0) cc_final: 0.7911 (t0) REVERT: B 502 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6079 (pmt-80) REVERT: B 504 TYR cc_start: 0.5784 (OUTLIER) cc_final: 0.4993 (t80) REVERT: B 521 ASN cc_start: 0.7695 (t0) cc_final: 0.6972 (t0) REVERT: B 540 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8128 (tmtm) REVERT: B 758 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9001 (tp) REVERT: B 930 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8259 (mmm) REVERT: B 936 MET cc_start: 0.3971 (pmm) cc_final: 0.3693 (pmm) REVERT: C 119 ASP cc_start: 0.7603 (m-30) cc_final: 0.6831 (p0) REVERT: C 269 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7105 (pt) REVERT: D 61 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7309 (mmp-170) REVERT: D 107 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.5958 (t80) REVERT: D 134 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7267 (p90) REVERT: D 237 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8423 (mppt) REVERT: D 274 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7832 (tp) REVERT: E 26 ASP cc_start: 0.8317 (t0) cc_final: 0.8055 (t0) REVERT: E 28 GLU cc_start: 0.7973 (mp0) cc_final: 0.7342 (mt-10) REVERT: E 37 LYS cc_start: 0.7517 (tptm) cc_final: 0.7051 (ttpt) outliers start: 99 outliers final: 40 residues processed: 347 average time/residue: 1.1937 time to fit residues: 481.2345 Evaluate side-chains 322 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 265 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 856 PHE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 349 HIS B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21923 Z= 0.244 Angle : 0.508 8.453 29610 Z= 0.263 Chirality : 0.040 0.243 3164 Planarity : 0.003 0.042 3744 Dihedral : 8.262 87.497 3051 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.97 % Allowed : 27.42 % Favored : 68.61 % 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: 0.83 (0.16), residues: 2517 helix: 1.09 (0.13), residues: 1525 sheet: -0.44 (0.57), residues: 75 loop : -0.14 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 60 HIS 0.011 0.001 HIS B 349 PHE 0.019 0.001 PHE B 942 TYR 0.016 0.001 TYR A 709 ARG 0.006 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 282 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8030 (mm) cc_final: 0.7714 (mm) REVERT: A 134 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: A 386 ASN cc_start: 0.7991 (m110) cc_final: 0.7722 (m110) REVERT: A 436 TYR cc_start: 0.8389 (t80) cc_final: 0.8095 (t80) REVERT: A 517 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.7915 (mtm110) REVERT: A 674 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7909 (t70) REVERT: A 784 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7135 (mp0) REVERT: A 787 ILE cc_start: 0.6432 (OUTLIER) cc_final: 0.6169 (tt) REVERT: A 844 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7462 (mp) REVERT: A 856 PHE cc_start: 0.5403 (OUTLIER) cc_final: 0.4702 (t80) REVERT: A 936 MET cc_start: 0.5136 (OUTLIER) cc_final: 0.3815 (mmt) REVERT: A 961 ASN cc_start: 0.8450 (m110) cc_final: 0.8230 (m110) REVERT: A 974 LYS cc_start: 0.7885 (pptt) cc_final: 0.7242 (pmmt) REVERT: B 17 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6626 (tp30) REVERT: B 54 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8186 (m) REVERT: B 69 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: B 83 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7409 (mm-30) REVERT: B 188 ASP cc_start: 0.8711 (m-30) cc_final: 0.8387 (m-30) REVERT: B 222 ASP cc_start: 0.8172 (t0) cc_final: 0.7884 (t0) REVERT: B 502 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6078 (pmt-80) REVERT: B 504 TYR cc_start: 0.5779 (OUTLIER) cc_final: 0.4973 (t80) REVERT: B 521 ASN cc_start: 0.7704 (t0) cc_final: 0.6992 (t0) REVERT: B 540 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8123 (tmtm) REVERT: B 758 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9029 (tp) REVERT: B 913 MET cc_start: 0.8082 (mmm) cc_final: 0.7765 (mmt) REVERT: B 936 MET cc_start: 0.3921 (pmm) cc_final: 0.3664 (pmm) REVERT: C 84 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7331 (m-10) REVERT: C 119 ASP cc_start: 0.7596 (m-30) cc_final: 0.6839 (p0) REVERT: C 269 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7129 (pt) REVERT: D 107 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.5947 (t80) REVERT: D 134 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7366 (p90) REVERT: D 212 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7632 (p) REVERT: D 237 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8413 (mppt) REVERT: D 274 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7863 (tp) REVERT: E 26 ASP cc_start: 0.8274 (t0) cc_final: 0.7997 (t0) REVERT: E 28 GLU cc_start: 0.7980 (mp0) cc_final: 0.7385 (mt-10) REVERT: E 37 LYS cc_start: 0.7518 (tptm) cc_final: 0.7036 (ttpt) outliers start: 93 outliers final: 40 residues processed: 346 average time/residue: 1.1931 time to fit residues: 478.9348 Evaluate side-chains 322 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 263 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 856 PHE Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 236 GLN B 349 HIS B 765 ASN B 797 ASN B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21923 Z= 0.268 Angle : 0.528 8.781 29610 Z= 0.273 Chirality : 0.040 0.241 3164 Planarity : 0.003 0.041 3744 Dihedral : 8.170 85.954 3050 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.09 % Allowed : 27.46 % Favored : 68.44 % 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: 0.76 (0.16), residues: 2517 helix: 1.04 (0.13), residues: 1525 sheet: -0.46 (0.56), residues: 75 loop : -0.19 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 60 HIS 0.011 0.001 HIS B 349 PHE 0.031 0.002 PHE B 942 TYR 0.024 0.001 TYR A 324 ARG 0.007 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 277 time to evaluate : 2.484 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7740 (mmt90) cc_final: 0.7143 (mpp-170) REVERT: A 62 LEU cc_start: 0.8030 (mm) cc_final: 0.7708 (mm) REVERT: A 134 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.6491 (m-80) REVERT: A 370 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6796 (mmt90) REVERT: A 386 ASN cc_start: 0.8016 (m110) cc_final: 0.7744 (m110) REVERT: A 517 ARG cc_start: 0.8501 (ttp-110) cc_final: 0.7897 (mtm110) REVERT: A 674 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7799 (t70) REVERT: A 784 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7216 (mp0) REVERT: A 787 ILE cc_start: 0.6462 (OUTLIER) cc_final: 0.6207 (tt) REVERT: A 844 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7480 (mp) REVERT: A 936 MET cc_start: 0.5090 (OUTLIER) cc_final: 0.3770 (mmt) REVERT: A 961 ASN cc_start: 0.8457 (m110) cc_final: 0.8235 (m110) REVERT: A 974 LYS cc_start: 0.7886 (pptt) cc_final: 0.7237 (pmmt) REVERT: B 17 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6749 (tp30) REVERT: B 54 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.8190 (m) REVERT: B 65 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7815 (mmtp) REVERT: B 69 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: B 188 ASP cc_start: 0.8702 (m-30) cc_final: 0.8378 (m-30) REVERT: B 222 ASP cc_start: 0.8175 (t0) cc_final: 0.7866 (t0) REVERT: B 502 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6122 (pmt-80) REVERT: B 504 TYR cc_start: 0.5782 (OUTLIER) cc_final: 0.4978 (t80) REVERT: B 521 ASN cc_start: 0.7683 (t0) cc_final: 0.6927 (t0) REVERT: B 540 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8157 (tmtm) REVERT: B 758 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9031 (tp) REVERT: B 913 MET cc_start: 0.8037 (mmm) cc_final: 0.7736 (mmt) REVERT: C 84 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7283 (m-10) REVERT: C 119 ASP cc_start: 0.7580 (m-30) cc_final: 0.6829 (p0) REVERT: C 269 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7103 (pt) REVERT: D 79 TYR cc_start: 0.3983 (m-10) cc_final: 0.3555 (m-10) REVERT: D 107 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.5907 (t80) REVERT: D 134 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7437 (p90) REVERT: D 212 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7627 (p) REVERT: D 237 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8417 (mppt) REVERT: D 274 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7843 (tp) REVERT: E 26 ASP cc_start: 0.8286 (t0) cc_final: 0.7982 (t0) REVERT: E 28 GLU cc_start: 0.8077 (mp0) cc_final: 0.7871 (mp0) REVERT: E 34 SER cc_start: 0.7908 (OUTLIER) cc_final: 0.7624 (m) REVERT: E 37 LYS cc_start: 0.7512 (tptm) cc_final: 0.7026 (ttpt) outliers start: 96 outliers final: 41 residues processed: 343 average time/residue: 1.2013 time to fit residues: 480.8547 Evaluate side-chains 326 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 265 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 504 TYR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 236 GLN B 349 HIS B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21923 Z= 0.203 Angle : 0.513 9.719 29610 Z= 0.265 Chirality : 0.039 0.241 3164 Planarity : 0.003 0.040 3744 Dihedral : 7.970 86.091 3049 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.01 % Allowed : 27.29 % Favored : 68.70 % 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: 0.85 (0.16), residues: 2517 helix: 1.13 (0.13), residues: 1518 sheet: -0.38 (0.58), residues: 75 loop : -0.16 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 60 HIS 0.011 0.001 HIS B 349 PHE 0.026 0.001 PHE B 942 TYR 0.019 0.001 TYR A 324 ARG 0.007 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 286 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7722 (mtt90) cc_final: 0.7152 (mpp-170) REVERT: A 62 LEU cc_start: 0.7995 (mm) cc_final: 0.7691 (mm) REVERT: A 134 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.6352 (m-80) REVERT: A 236 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7122 (mm110) REVERT: A 335 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8200 (mp0) REVERT: A 386 ASN cc_start: 0.8029 (m110) cc_final: 0.7761 (m110) REVERT: A 436 TYR cc_start: 0.8085 (t80) cc_final: 0.7809 (t80) REVERT: A 517 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.7905 (mtm110) REVERT: A 674 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7836 (t70) REVERT: A 784 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7218 (mp0) REVERT: A 787 ILE cc_start: 0.6429 (OUTLIER) cc_final: 0.6166 (tt) REVERT: A 844 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7466 (mp) REVERT: A 936 MET cc_start: 0.5159 (OUTLIER) cc_final: 0.3806 (mmt) REVERT: A 961 ASN cc_start: 0.8453 (m110) cc_final: 0.8234 (m110) REVERT: A 974 LYS cc_start: 0.7838 (pptt) cc_final: 0.7218 (pmmt) REVERT: B 17 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6674 (tp30) REVERT: B 188 ASP cc_start: 0.8603 (m-30) cc_final: 0.8288 (m-30) REVERT: B 222 ASP cc_start: 0.8095 (t0) cc_final: 0.7805 (t0) REVERT: B 502 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6070 (pmt-80) REVERT: B 521 ASN cc_start: 0.7680 (t0) cc_final: 0.6910 (t0) REVERT: B 540 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8135 (tmtm) REVERT: B 758 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8999 (tp) REVERT: B 913 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7696 (mmt) REVERT: B 936 MET cc_start: 0.3609 (pmm) cc_final: 0.3256 (pmm) REVERT: C 84 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7269 (m-10) REVERT: C 119 ASP cc_start: 0.7387 (m-30) cc_final: 0.6674 (p0) REVERT: C 134 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.6741 (p90) REVERT: C 145 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7184 (tmt90) REVERT: C 165 ARG cc_start: 0.7507 (ptm160) cc_final: 0.7142 (ptm160) REVERT: C 269 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7108 (pt) REVERT: D 79 TYR cc_start: 0.3970 (m-10) cc_final: 0.3587 (m-10) REVERT: D 82 ASP cc_start: 0.7335 (m-30) cc_final: 0.6982 (p0) REVERT: D 107 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.5880 (t80) REVERT: D 134 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7307 (p90) REVERT: D 212 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7641 (p) REVERT: D 237 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8406 (mppt) REVERT: D 274 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7841 (tp) REVERT: E 20 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7808 (pt) REVERT: E 26 ASP cc_start: 0.8269 (t0) cc_final: 0.7969 (t0) REVERT: E 28 GLU cc_start: 0.8065 (mp0) cc_final: 0.7818 (mp0) REVERT: E 34 SER cc_start: 0.7915 (OUTLIER) cc_final: 0.7653 (m) REVERT: E 37 LYS cc_start: 0.7522 (tptm) cc_final: 0.7026 (ttpt) outliers start: 94 outliers final: 42 residues processed: 350 average time/residue: 1.2050 time to fit residues: 491.0011 Evaluate side-chains 329 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 266 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 191 optimal weight: 0.0010 chunk 221 optimal weight: 3.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 115 ASN B 236 GLN B 349 HIS B 797 ASN B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21923 Z= 0.260 Angle : 0.533 10.043 29610 Z= 0.274 Chirality : 0.040 0.246 3164 Planarity : 0.003 0.040 3744 Dihedral : 7.936 86.623 3047 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.62 % Allowed : 27.97 % Favored : 68.40 % 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: 0.73 (0.16), residues: 2517 helix: 1.04 (0.13), residues: 1522 sheet: -0.41 (0.57), residues: 75 loop : -0.22 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 60 HIS 0.012 0.001 HIS B 349 PHE 0.029 0.001 PHE B 942 TYR 0.019 0.001 TYR A 324 ARG 0.008 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 276 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8033 (mm) cc_final: 0.7721 (mm) REVERT: A 134 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.6609 (m-80) REVERT: A 236 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7215 (mm110) REVERT: A 295 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7363 (mt-10) REVERT: A 370 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6778 (mmt90) REVERT: A 436 TYR cc_start: 0.8297 (t80) cc_final: 0.8015 (t80) REVERT: A 517 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.7881 (mtm110) REVERT: A 525 ASP cc_start: 0.8339 (m-30) cc_final: 0.8072 (m-30) REVERT: A 674 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7818 (t70) REVERT: A 784 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7210 (mp0) REVERT: A 787 ILE cc_start: 0.6448 (OUTLIER) cc_final: 0.6193 (tt) REVERT: A 844 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7477 (mp) REVERT: A 936 MET cc_start: 0.5116 (OUTLIER) cc_final: 0.3813 (mmt) REVERT: A 961 ASN cc_start: 0.8462 (m110) cc_final: 0.8240 (m110) REVERT: A 974 LYS cc_start: 0.7893 (pptt) cc_final: 0.7248 (pmmt) REVERT: B 17 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6691 (tp30) REVERT: B 69 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: B 188 ASP cc_start: 0.8622 (m-30) cc_final: 0.8298 (m-30) REVERT: B 222 ASP cc_start: 0.8150 (t0) cc_final: 0.7851 (t0) REVERT: B 502 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6057 (pmt-80) REVERT: B 521 ASN cc_start: 0.7704 (t0) cc_final: 0.6972 (t0) REVERT: B 540 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8111 (tmtm) REVERT: B 758 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9032 (tp) REVERT: B 913 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7703 (mmt) REVERT: B 936 MET cc_start: 0.3623 (pmm) cc_final: 0.3237 (pmm) REVERT: B 948 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8203 (t0) REVERT: C 84 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7238 (m-10) REVERT: C 119 ASP cc_start: 0.7382 (m-30) cc_final: 0.6643 (p0) REVERT: C 134 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.6729 (p90) REVERT: C 145 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7188 (tmt90) REVERT: C 165 ARG cc_start: 0.7516 (ptm160) cc_final: 0.7155 (ptm160) REVERT: C 269 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7083 (pt) REVERT: D 82 ASP cc_start: 0.7352 (m-30) cc_final: 0.7005 (p0) REVERT: D 134 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7388 (p90) REVERT: D 212 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7625 (p) REVERT: D 237 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8416 (mppt) REVERT: D 247 ARG cc_start: 0.7382 (ttt-90) cc_final: 0.6787 (ttt-90) REVERT: D 274 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7848 (tp) REVERT: E 20 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7887 (pt) REVERT: E 26 ASP cc_start: 0.8279 (t0) cc_final: 0.7993 (t0) REVERT: E 34 SER cc_start: 0.7921 (OUTLIER) cc_final: 0.7673 (m) REVERT: E 37 LYS cc_start: 0.7512 (tptm) cc_final: 0.7046 (ttpt) REVERT: E 41 LYS cc_start: 0.7385 (mttm) cc_final: 0.6958 (mmpt) outliers start: 85 outliers final: 40 residues processed: 337 average time/residue: 1.2753 time to fit residues: 506.1489 Evaluate side-chains 328 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 265 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 178 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 226 optimal weight: 0.2980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 236 GLN B 349 HIS B 948 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21923 Z= 0.182 Angle : 0.518 10.865 29610 Z= 0.267 Chirality : 0.039 0.244 3164 Planarity : 0.003 0.040 3744 Dihedral : 7.760 86.367 3047 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.54 % Allowed : 28.27 % Favored : 68.19 % 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: 0.89 (0.16), residues: 2517 helix: 1.15 (0.13), residues: 1515 sheet: -0.32 (0.61), residues: 68 loop : -0.15 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 60 HIS 0.012 0.001 HIS B 349 PHE 0.027 0.001 PHE B 942 TYR 0.027 0.001 TYR A 324 ARG 0.008 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 277 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7750 (mmt90) cc_final: 0.7142 (mpp-170) REVERT: A 62 LEU cc_start: 0.7999 (mm) cc_final: 0.7689 (mm) REVERT: A 134 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.6344 (m-80) REVERT: A 236 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7199 (mm110) REVERT: A 335 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8187 (mp0) REVERT: A 436 TYR cc_start: 0.8187 (t80) cc_final: 0.7902 (t80) REVERT: A 517 ARG cc_start: 0.8491 (ttp-110) cc_final: 0.7894 (mtm110) REVERT: A 525 ASP cc_start: 0.8333 (m-30) cc_final: 0.8068 (m-30) REVERT: A 674 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7860 (t70) REVERT: A 784 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7236 (mp0) REVERT: A 787 ILE cc_start: 0.6381 (OUTLIER) cc_final: 0.6113 (tt) REVERT: A 844 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7506 (mp) REVERT: A 936 MET cc_start: 0.5156 (OUTLIER) cc_final: 0.3887 (mmt) REVERT: A 961 ASN cc_start: 0.8395 (m110) cc_final: 0.8179 (m110) REVERT: A 974 LYS cc_start: 0.7778 (pptt) cc_final: 0.7170 (pmmt) REVERT: B 17 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6689 (tp30) REVERT: B 28 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8025 (mm-30) REVERT: B 69 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: B 188 ASP cc_start: 0.8570 (m-30) cc_final: 0.8242 (m-30) REVERT: B 222 ASP cc_start: 0.8057 (t0) cc_final: 0.7764 (t0) REVERT: B 306 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6587 (t0) REVERT: B 502 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6074 (pmt-80) REVERT: B 521 ASN cc_start: 0.7724 (t0) cc_final: 0.7002 (t0) REVERT: B 540 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8112 (tmtm) REVERT: B 758 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8997 (tp) REVERT: B 936 MET cc_start: 0.3799 (pmm) cc_final: 0.3447 (pmm) REVERT: C 84 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7218 (m-10) REVERT: C 119 ASP cc_start: 0.7280 (m-30) cc_final: 0.6577 (p0) REVERT: C 134 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.6631 (p90) REVERT: C 145 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7175 (tmt90) REVERT: C 165 ARG cc_start: 0.7491 (ptm160) cc_final: 0.7133 (ptm160) REVERT: C 269 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.7080 (pt) REVERT: D 82 ASP cc_start: 0.7296 (m-30) cc_final: 0.6958 (p0) REVERT: D 134 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7482 (p90) REVERT: D 212 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7614 (p) REVERT: D 237 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8405 (mppt) REVERT: D 247 ARG cc_start: 0.7310 (ttt-90) cc_final: 0.6622 (ttt-90) REVERT: D 274 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7799 (tp) REVERT: E 20 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7763 (pt) REVERT: E 26 ASP cc_start: 0.8288 (t0) cc_final: 0.7983 (t0) REVERT: E 28 GLU cc_start: 0.7843 (mp0) cc_final: 0.7224 (mt-10) REVERT: E 34 SER cc_start: 0.7929 (OUTLIER) cc_final: 0.7681 (m) REVERT: E 37 LYS cc_start: 0.7539 (tptm) cc_final: 0.7048 (ttpt) REVERT: E 41 LYS cc_start: 0.7414 (mttm) cc_final: 0.7040 (mmpt) outliers start: 83 outliers final: 34 residues processed: 336 average time/residue: 1.1748 time to fit residues: 459.2135 Evaluate side-chains 322 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 267 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 0.0070 chunk 146 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 167 optimal weight: 0.0980 chunk 252 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 200 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 0.4980 chunk 159 optimal weight: 0.2980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 236 GLN B 349 HIS B 797 ASN B 948 ASN C 182 ASN C 224 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21923 Z= 0.146 Angle : 0.503 11.518 29610 Z= 0.258 Chirality : 0.039 0.245 3164 Planarity : 0.003 0.040 3744 Dihedral : 7.410 86.839 3043 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.52 % Allowed : 29.47 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.17), residues: 2517 helix: 1.27 (0.14), residues: 1520 sheet: -0.22 (0.62), residues: 68 loop : -0.11 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 919 HIS 0.012 0.001 HIS B 349 PHE 0.023 0.001 PHE B 942 TYR 0.021 0.001 TYR A 324 ARG 0.008 0.000 ARG C 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 294 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7716 (mmt90) cc_final: 0.7120 (mpp-170) REVERT: A 62 LEU cc_start: 0.7982 (mm) cc_final: 0.7680 (mm) REVERT: A 134 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.6083 (m-80) REVERT: A 236 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7164 (mm110) REVERT: A 407 ILE cc_start: 0.8165 (mp) cc_final: 0.7879 (mt) REVERT: A 436 TYR cc_start: 0.8020 (t80) cc_final: 0.7776 (t80) REVERT: A 517 ARG cc_start: 0.8485 (ttp-110) cc_final: 0.7898 (mtm110) REVERT: A 525 ASP cc_start: 0.8348 (m-30) cc_final: 0.8081 (m-30) REVERT: A 674 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7920 (t70) REVERT: A 784 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7237 (mp0) REVERT: A 787 ILE cc_start: 0.6379 (OUTLIER) cc_final: 0.6104 (tt) REVERT: A 844 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7504 (mp) REVERT: A 936 MET cc_start: 0.5071 (mpt) cc_final: 0.3808 (mmt) REVERT: A 961 ASN cc_start: 0.8408 (m110) cc_final: 0.8202 (m110) REVERT: A 974 LYS cc_start: 0.7544 (pptt) cc_final: 0.7007 (pmmt) REVERT: B 17 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6669 (tp30) REVERT: B 69 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: B 188 ASP cc_start: 0.8557 (m-30) cc_final: 0.8241 (m-30) REVERT: B 222 ASP cc_start: 0.8081 (t0) cc_final: 0.7816 (t0) REVERT: B 223 TYR cc_start: 0.8692 (t80) cc_final: 0.8410 (t80) REVERT: B 306 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6483 (t0) REVERT: B 502 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6064 (pmt-80) REVERT: B 521 ASN cc_start: 0.7741 (t0) cc_final: 0.7019 (t0) REVERT: B 540 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8057 (tmtm) REVERT: B 888 TYR cc_start: 0.7846 (t80) cc_final: 0.7610 (t80) REVERT: B 936 MET cc_start: 0.3782 (pmm) cc_final: 0.3477 (pmm) REVERT: C 84 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7218 (m-80) REVERT: C 119 ASP cc_start: 0.7353 (m-30) cc_final: 0.6609 (p0) REVERT: C 134 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.6534 (p90) REVERT: C 145 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7310 (tmt90) REVERT: C 165 ARG cc_start: 0.7414 (ptm160) cc_final: 0.7054 (ptm160) REVERT: C 269 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.7050 (pt) REVERT: D 82 ASP cc_start: 0.7259 (m-30) cc_final: 0.7031 (p0) REVERT: D 134 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7400 (p90) REVERT: D 237 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8381 (mppt) REVERT: D 247 ARG cc_start: 0.7153 (ttt-90) cc_final: 0.6501 (ttt-90) REVERT: E 20 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7668 (pt) REVERT: E 26 ASP cc_start: 0.8249 (t0) cc_final: 0.7985 (t0) REVERT: E 28 GLU cc_start: 0.7826 (mp0) cc_final: 0.7235 (mt-10) REVERT: E 34 SER cc_start: 0.7959 (OUTLIER) cc_final: 0.7717 (m) REVERT: E 37 LYS cc_start: 0.7557 (tptm) cc_final: 0.7051 (ttpt) REVERT: E 41 LYS cc_start: 0.7456 (mttm) cc_final: 0.7081 (mmpt) REVERT: E 52 ARG cc_start: 0.6832 (ttt-90) cc_final: 0.6570 (ptm160) outliers start: 59 outliers final: 28 residues processed: 334 average time/residue: 1.2259 time to fit residues: 472.9882 Evaluate side-chains 314 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 269 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 201 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 206 optimal weight: 0.5980 chunk 25 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 236 GLN B 349 HIS D 115 ASN D 118 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.149656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117715 restraints weight = 31495.693| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.11 r_work: 0.3325 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21923 Z= 0.169 Angle : 0.505 12.539 29610 Z= 0.259 Chirality : 0.039 0.242 3164 Planarity : 0.003 0.040 3744 Dihedral : 7.379 87.045 3043 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.56 % Allowed : 29.77 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.16), residues: 2517 helix: 1.25 (0.13), residues: 1524 sheet: -0.19 (0.61), residues: 68 loop : -0.11 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 919 HIS 0.014 0.001 HIS B 349 PHE 0.022 0.001 PHE B 942 TYR 0.022 0.001 TYR A 324 ARG 0.008 0.000 ARG C 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8466.00 seconds wall clock time: 153 minutes 57.87 seconds (9237.87 seconds total)