Starting phenix.real_space_refine on Sun Mar 17 07:38:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/03_2024/7whp_32507_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/03_2024/7whp_32507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/03_2024/7whp_32507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/03_2024/7whp_32507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/03_2024/7whp_32507_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whp_32507/03_2024/7whp_32507_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 6 5.49 5 S 94 5.16 5 C 10770 2.51 5 N 2948 2.21 5 O 3220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 898": "OE1" <-> "OE2" Residue "B GLU 1023": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17038 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8434 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 5, 'PTRANS': 47, 'TRANS': 1004} Chain: "B" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8434 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 1004} Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'ATP': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="SAM A1102 " pdbres="ATP A1103 " Chain breaks: 1 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'ATP': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="SAM B1102 " pdbres="ATP B1103 " Chain breaks: 1 Time building chain proxies: 9.07, per 1000 atoms: 0.53 Number of scatterers: 17038 At special positions: 0 Unit cell: (160.362, 107.262, 204.966, 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 94 16.00 P 6 15.00 O 3220 8.00 N 2948 7.00 C 10770 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: 6.52 Conformation dependent library (CDL) restraints added in 3.0 seconds 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 22 sheets defined 35.0% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 11 through 14 No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 20 through 26 removed outlier: 4.371A pdb=" N ARG A 23 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 26 " --> pdb=" O ARG A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.895A pdb=" N SER A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.705A pdb=" N ASN A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 141 Processing helix chain 'A' and resid 146 through 157 removed outlier: 4.063A pdb=" N PHE A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.578A pdb=" N ARG A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 224 through 246 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 330 through 342 removed outlier: 3.946A pdb=" N LEU A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.809A pdb=" N LEU A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 Processing helix chain 'A' and resid 467 through 479 Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 530 through 542 Processing helix chain 'A' and resid 567 through 575 Processing helix chain 'A' and resid 625 through 642 Processing helix chain 'A' and resid 655 through 666 removed outlier: 3.602A pdb=" N SER A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 716 No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'A' and resid 752 through 764 Proline residue: A 756 - end of helix removed outlier: 3.700A pdb=" N LYS A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 810 removed outlier: 4.186A pdb=" N ARG A 810 " --> pdb=" O HIS A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 851 Processing helix chain 'A' and resid 867 through 870 removed outlier: 4.332A pdb=" N SER A 870 " --> pdb=" O ALA A 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 867 through 870' Processing helix chain 'A' and resid 889 through 893 Processing helix chain 'A' and resid 936 through 950 Processing helix chain 'A' and resid 965 through 971 removed outlier: 3.508A pdb=" N ILE A 968 " --> pdb=" O ALA A 965 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 969 " --> pdb=" O GLY A 966 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 971 " --> pdb=" O ILE A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1010 Processing helix chain 'A' and resid 1021 through 1030 Processing helix chain 'A' and resid 1037 through 1048 removed outlier: 4.372A pdb=" N ALA A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A1044 " --> pdb=" O GLY A1040 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS A1048 " --> pdb=" O ASP A1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 19 through 25 removed outlier: 4.483A pdb=" N ARG B 23 " --> pdb=" O ASN B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 85 through 98 removed outlier: 3.623A pdb=" N SER B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.757A pdb=" N ARG B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 138 through 141 removed outlier: 3.543A pdb=" N LEU B 141 " --> pdb=" O PRO B 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 141' Processing helix chain 'B' and resid 147 through 157 removed outlier: 3.555A pdb=" N ASN B 151 " --> pdb=" O ASP B 148 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER B 152 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 155 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 199 removed outlier: 3.746A pdb=" N HIS B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 224 through 247 removed outlier: 3.700A pdb=" N ASP B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 278 removed outlier: 4.002A pdb=" N LEU B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 284 No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 293 through 306 removed outlier: 3.593A pdb=" N THR B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.797A pdb=" N LEU B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 431 through 446 removed outlier: 3.525A pdb=" N ASP B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 443 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 459 Processing helix chain 'B' and resid 462 through 465 No H-bonds generated for 'chain 'B' and resid 462 through 465' Processing helix chain 'B' and resid 467 through 479 removed outlier: 3.655A pdb=" N LYS B 479 " --> pdb=" O ARG B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 529 through 542 removed outlier: 3.614A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 575 Processing helix chain 'B' and resid 625 through 641 Processing helix chain 'B' and resid 655 through 665 removed outlier: 3.631A pdb=" N ILE B 662 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 717 removed outlier: 3.810A pdb=" N ARG B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N TYR B 715 " --> pdb=" O MET B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 764 Proline residue: B 756 - end of helix removed outlier: 3.626A pdb=" N LEU B 759 " --> pdb=" O PRO B 756 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 762 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS B 763 " --> pdb=" O SER B 760 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 764 " --> pdb=" O GLN B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 811 removed outlier: 3.502A pdb=" N GLN B 809 " --> pdb=" O TYR B 805 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG B 810 " --> pdb=" O HIS B 806 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR B 811 " --> pdb=" O GLU B 807 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 805 through 811' Processing helix chain 'B' and resid 833 through 851 removed outlier: 3.578A pdb=" N LEU B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 870 removed outlier: 4.355A pdb=" N SER B 870 " --> pdb=" O ALA B 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 867 through 870' Processing helix chain 'B' and resid 889 through 894 removed outlier: 3.549A pdb=" N LYS B 894 " --> pdb=" O LEU B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 950 Processing helix chain 'B' and resid 965 through 973 removed outlier: 3.993A pdb=" N ASP B 972 " --> pdb=" O THR B 969 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 973 " --> pdb=" O ARG B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1010 Processing helix chain 'B' and resid 1021 through 1030 Processing helix chain 'B' and resid 1037 through 1048 removed outlier: 4.082A pdb=" N ALA B1041 " --> pdb=" O SER B1037 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP B1044 " --> pdb=" O GLY B1040 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B1045 " --> pdb=" O ALA B1041 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B1048 " --> pdb=" O ASP B1044 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.878A pdb=" N VAL A 251 " --> pdb=" O THR A 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.614A pdb=" N THR A 41 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 50 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 43 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 48 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 161 through 165 Processing sheet with id= D, first strand: chain 'A' and resid 326 through 329 Processing sheet with id= E, first strand: chain 'A' and resid 401 through 404 removed outlier: 6.195A pdb=" N THR A 823 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER A 404 " --> pdb=" O THR A 823 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU A 825 " --> pdb=" O SER A 404 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 419 through 423 removed outlier: 3.918A pdb=" N THR A 690 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 556 through 560 removed outlier: 5.922A pdb=" N ARG A 583 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 559 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 585 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 729 through 731 removed outlier: 3.583A pdb=" N CYS A 747 " --> pdb=" O HIS A 731 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 858 through 860 removed outlier: 8.094A pdb=" N VAL A 859 " --> pdb=" O ASN A 916 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 918 " --> pdb=" O VAL A 859 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN A 955 " --> pdb=" O SER A 917 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N TYR A 919 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 957 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE A 921 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR A 959 " --> pdb=" O PHE A 921 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 962 " --> pdb=" O PRO A1051 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 879 through 881 removed outlier: 6.474A pdb=" N GLU A 898 " --> pdb=" O VAL A 880 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 980 through 983 Processing sheet with id= L, first strand: chain 'A' and resid 205 through 207 removed outlier: 7.034A pdb=" N THR A 207 " --> pdb=" O PRO A 262 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 5 through 8 removed outlier: 4.027A pdb=" N VAL B 251 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 7 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 38 through 43 Processing sheet with id= O, first strand: chain 'B' and resid 161 through 165 Processing sheet with id= P, first strand: chain 'B' and resid 326 through 329 removed outlier: 3.579A pdb=" N PHE B 355 " --> pdb=" O MET B 328 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 373 through 376 removed outlier: 5.509A pdb=" N GLU B 768 " --> pdb=" O ARG B 786 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG B 786 " --> pdb=" O GLU B 768 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 401 through 404 removed outlier: 6.167A pdb=" N THR B 823 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N SER B 404 " --> pdb=" O THR B 823 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU B 825 " --> pdb=" O SER B 404 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'B' and resid 419 through 423 removed outlier: 6.808A pdb=" N ILE B 613 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LYS B 649 " --> pdb=" O ILE B 613 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N CYS B 615 " --> pdb=" O LYS B 649 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 614 " --> pdb=" O ILE B 558 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1052 through 1056 removed outlier: 3.706A pdb=" N SER B 917 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLN B 857 " --> pdb=" O ILE B 918 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N LEU B 920 " --> pdb=" O GLN B 857 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 859 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS B 877 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N SER B 860 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 879 " --> pdb=" O SER B 860 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 980 through 982 Processing sheet with id= V, first strand: chain 'B' and resid 205 through 207 removed outlier: 7.109A pdb=" N THR B 207 " --> pdb=" O PRO B 262 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1434 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: 6.26 Time building geometry restraints manager: 7.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5561 1.34 - 1.46: 2638 1.46 - 1.57: 9035 1.57 - 1.69: 10 1.69 - 1.81: 176 Bond restraints: 17420 Sorted by residual: bond pdb=" C2 SAM A1102 " pdb=" N3 SAM A1102 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" C2 SAM B1101 " pdb=" N3 SAM B1101 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.10e+00 bond pdb=" C2 SAM A1101 " pdb=" N3 SAM A1101 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" C2 SAM B1102 " pdb=" N3 SAM B1102 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" C8 SAM B1102 " pdb=" N7 SAM B1102 " ideal model delta sigma weight residual 1.298 1.352 -0.054 2.00e-02 2.50e+03 7.21e+00 ... (remaining 17415 not shown) Histogram of bond angle deviations from ideal: 99.22 - 107.36: 708 107.36 - 115.50: 10736 115.50 - 123.64: 11842 123.64 - 131.77: 427 131.77 - 139.91: 33 Bond angle restraints: 23746 Sorted by residual: angle pdb=" C ILE B 519 " pdb=" N PRO B 520 " pdb=" CA PRO B 520 " ideal model delta sigma weight residual 120.52 112.93 7.59 9.90e-01 1.02e+00 5.89e+01 angle pdb=" N GLU A 564 " pdb=" CA GLU A 564 " pdb=" C GLU A 564 " ideal model delta sigma weight residual 110.97 106.77 4.20 1.09e+00 8.42e-01 1.49e+01 angle pdb=" N GLU A 566 " pdb=" CA GLU A 566 " pdb=" C GLU A 566 " ideal model delta sigma weight residual 109.42 114.97 -5.55 1.48e+00 4.57e-01 1.41e+01 angle pdb=" N ARG A 112 " pdb=" CA ARG A 112 " pdb=" C ARG A 112 " ideal model delta sigma weight residual 109.23 103.84 5.39 1.55e+00 4.16e-01 1.21e+01 angle pdb=" CB LYS A 244 " pdb=" CG LYS A 244 " pdb=" CD LYS A 244 " ideal model delta sigma weight residual 111.30 118.15 -6.85 2.30e+00 1.89e-01 8.86e+00 ... (remaining 23741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 9405 17.67 - 35.33: 989 35.33 - 53.00: 210 53.00 - 70.67: 26 70.67 - 88.34: 22 Dihedral angle restraints: 10652 sinusoidal: 4356 harmonic: 6296 Sorted by residual: dihedral pdb=" CA LEU A 816 " pdb=" C LEU A 816 " pdb=" N GLY A 817 " pdb=" CA GLY A 817 " ideal model delta harmonic sigma weight residual -180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA LEU A 551 " pdb=" C LEU A 551 " pdb=" N MET A 552 " pdb=" CA MET A 552 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG B 590 " pdb=" CD ARG B 590 " pdb=" NE ARG B 590 " pdb=" CZ ARG B 590 " ideal model delta sinusoidal sigma weight residual -180.00 -135.13 -44.87 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 10649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1937 0.042 - 0.083: 568 0.083 - 0.125: 207 0.125 - 0.166: 24 0.166 - 0.208: 6 Chirality restraints: 2742 Sorted by residual: chirality pdb=" C1' SAM A1102 " pdb=" C2' SAM A1102 " pdb=" N9 SAM A1102 " pdb=" O4' SAM A1102 " both_signs ideal model delta sigma weight residual False 2.30 2.51 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PRO B 554 " pdb=" N PRO B 554 " pdb=" C PRO B 554 " pdb=" CB PRO B 554 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2' SAM B1102 " pdb=" C1' SAM B1102 " pdb=" C3' SAM B1102 " pdb=" O2' SAM B1102 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 2739 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 553 " -0.061 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO A 554 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 554 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 554 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 553 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B 554 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 554 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 554 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 74 " -0.047 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO A 75 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.039 5.00e-02 4.00e+02 ... (remaining 3019 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1728 2.75 - 3.29: 17080 3.29 - 3.82: 27371 3.82 - 4.36: 33342 4.36 - 4.90: 57237 Nonbonded interactions: 136758 Sorted by model distance: nonbonded pdb=" OG SER B 301 " pdb=" OH TYR B 316 " model vdw 2.209 2.440 nonbonded pdb=" O ARG B 324 " pdb=" OH TYR B 349 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR A 856 " pdb=" O ASN A 916 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR A 842 " pdb=" O SAM A1102 " model vdw 2.226 2.440 nonbonded pdb=" O VAL A 733 " pdb=" OH TYR A 741 " model vdw 2.228 2.440 ... (remaining 136753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.740 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 47.640 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 0.066 17420 Z= 0.239 Angle : 0.623 11.338 23746 Z= 0.305 Chirality : 0.045 0.208 2742 Planarity : 0.005 0.094 3022 Dihedral : 15.130 88.336 6576 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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 (0.18), residues: 2110 helix: -0.24 (0.18), residues: 826 sheet: -0.36 (0.32), residues: 286 loop : -0.78 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 2 HIS 0.005 0.001 HIS B 217 PHE 0.014 0.001 PHE A 456 TYR 0.024 0.001 TYR A 963 ARG 0.008 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.936 Fit side-chains revert: symmetry clash REVERT: A 865 ASN cc_start: 0.7830 (m-40) cc_final: 0.7431 (p0) REVERT: B 36 THR cc_start: 0.7805 (p) cc_final: 0.7532 (p) REVERT: B 286 ASN cc_start: 0.6816 (t0) cc_final: 0.6544 (t0) REVERT: B 855 MET cc_start: 0.7750 (tpp) cc_final: 0.7507 (tpp) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.3128 time to fit residues: 155.5916 Evaluate side-chains 293 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 190 optimal weight: 0.3980 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 339 GLN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 HIS ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17420 Z= 0.291 Angle : 0.577 7.251 23746 Z= 0.299 Chirality : 0.046 0.203 2742 Planarity : 0.005 0.086 3022 Dihedral : 8.620 87.909 2556 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 1.70 % Allowed : 9.08 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.74 (0.18), residues: 2110 helix: 0.01 (0.18), residues: 814 sheet: -0.35 (0.31), residues: 294 loop : -0.86 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.007 0.001 HIS A 217 PHE 0.010 0.001 PHE A 746 TYR 0.017 0.001 TYR B 474 ARG 0.005 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 317 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.8033 (t0) cc_final: 0.7766 (t0) REVERT: A 339 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7206 (mp10) REVERT: A 519 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6749 (pt) REVERT: A 865 ASN cc_start: 0.7723 (m-40) cc_final: 0.7356 (p0) REVERT: B 116 MET cc_start: 0.8496 (ttp) cc_final: 0.8108 (ttm) REVERT: B 286 ASN cc_start: 0.6656 (t0) cc_final: 0.6385 (t0) REVERT: B 316 TYR cc_start: 0.8209 (t80) cc_final: 0.7833 (t80) REVERT: B 474 TYR cc_start: 0.8127 (t80) cc_final: 0.7767 (t80) outliers start: 32 outliers final: 23 residues processed: 333 average time/residue: 0.3139 time to fit residues: 153.8690 Evaluate side-chains 318 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 294 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 868 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 191 optimal weight: 20.0000 chunk 206 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 153 optimal weight: 30.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 299 GLN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17420 Z= 0.234 Angle : 0.529 6.511 23746 Z= 0.274 Chirality : 0.044 0.201 2742 Planarity : 0.005 0.083 3022 Dihedral : 8.147 88.372 2556 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.82 % Rotamer: Outliers : 2.02 % Allowed : 13.96 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.68 (0.18), residues: 2110 helix: 0.14 (0.18), residues: 816 sheet: -0.60 (0.32), residues: 270 loop : -0.81 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 184 HIS 0.005 0.001 HIS A 217 PHE 0.010 0.001 PHE A 72 TYR 0.015 0.001 TYR A1049 ARG 0.003 0.000 ARG B 525 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 316 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7995 (t0) cc_final: 0.7728 (t0) REVERT: A 285 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.4567 (mp0) REVERT: A 716 MET cc_start: 0.8182 (mmt) cc_final: 0.7933 (mmt) REVERT: A 865 ASN cc_start: 0.7859 (m-40) cc_final: 0.7426 (p0) REVERT: B 286 ASN cc_start: 0.6670 (t0) cc_final: 0.6340 (t0) REVERT: B 316 TYR cc_start: 0.8170 (t80) cc_final: 0.7784 (t80) REVERT: B 474 TYR cc_start: 0.8155 (t80) cc_final: 0.7835 (t80) outliers start: 38 outliers final: 28 residues processed: 331 average time/residue: 0.3138 time to fit residues: 154.1670 Evaluate side-chains 325 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 296 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 866 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 339 GLN B 299 GLN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17420 Z= 0.360 Angle : 0.608 7.532 23746 Z= 0.314 Chirality : 0.047 0.204 2742 Planarity : 0.005 0.082 3022 Dihedral : 8.355 86.305 2556 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.31 % Favored : 95.64 % Rotamer: Outliers : 3.08 % Allowed : 16.03 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.94 (0.18), residues: 2110 helix: -0.09 (0.18), residues: 818 sheet: -0.70 (0.32), residues: 270 loop : -0.96 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 2 HIS 0.014 0.001 HIS A 3 PHE 0.012 0.002 PHE B 904 TYR 0.021 0.002 TYR A1049 ARG 0.005 0.000 ARG B1034 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 303 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.8036 (t0) cc_final: 0.7796 (t0) REVERT: A 285 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.4784 (mp0) REVERT: A 339 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7124 (mp10) REVERT: A 593 GLU cc_start: 0.5342 (OUTLIER) cc_final: 0.4786 (pm20) REVERT: A 824 ARG cc_start: 0.7962 (tpp-160) cc_final: 0.7689 (ttt90) REVERT: A 865 ASN cc_start: 0.7842 (m-40) cc_final: 0.7404 (p0) REVERT: B 286 ASN cc_start: 0.6704 (t0) cc_final: 0.6337 (t0) REVERT: B 316 TYR cc_start: 0.8187 (t80) cc_final: 0.7809 (t80) REVERT: B 474 TYR cc_start: 0.8099 (t80) cc_final: 0.7800 (t80) outliers start: 58 outliers final: 40 residues processed: 336 average time/residue: 0.3006 time to fit residues: 150.3905 Evaluate side-chains 334 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 292 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 907 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 182 optimal weight: 8.9990 chunk 51 optimal weight: 0.0060 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 623 GLN B 217 HIS B 299 GLN B 737 HIS B 761 GLN ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 17420 Z= 0.147 Angle : 0.474 5.778 23746 Z= 0.246 Chirality : 0.043 0.198 2742 Planarity : 0.004 0.080 3022 Dihedral : 7.683 86.416 2556 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Rotamer: Outliers : 2.28 % Allowed : 18.10 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.48 (0.18), residues: 2110 helix: 0.37 (0.19), residues: 804 sheet: -0.61 (0.32), residues: 270 loop : -0.70 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 772 HIS 0.011 0.001 HIS A 3 PHE 0.025 0.001 PHE A 283 TYR 0.017 0.001 TYR A 38 ARG 0.005 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 339 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8358 (mm) cc_final: 0.8137 (mm) REVERT: A 238 ASP cc_start: 0.7963 (t0) cc_final: 0.7697 (t0) REVERT: A 339 GLN cc_start: 0.7252 (mm-40) cc_final: 0.6900 (mp10) REVERT: A 386 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6984 (p0) REVERT: A 532 MET cc_start: 0.7987 (tpp) cc_final: 0.7701 (mmt) REVERT: A 824 ARG cc_start: 0.7894 (tpp-160) cc_final: 0.7610 (ttt90) REVERT: A 865 ASN cc_start: 0.7832 (m-40) cc_final: 0.7427 (p0) REVERT: A 1055 LEU cc_start: 0.8759 (mt) cc_final: 0.8454 (mt) REVERT: B 116 MET cc_start: 0.8727 (ttp) cc_final: 0.8500 (ttp) REVERT: B 270 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7444 (mm-40) REVERT: B 286 ASN cc_start: 0.6709 (t0) cc_final: 0.6325 (t0) REVERT: B 474 TYR cc_start: 0.8202 (t80) cc_final: 0.7870 (t80) outliers start: 43 outliers final: 32 residues processed: 362 average time/residue: 0.3101 time to fit residues: 168.0812 Evaluate side-chains 352 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 319 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 761 GLN Chi-restraints excluded: chain B residue 762 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 299 GLN B 737 HIS B 761 GLN B 806 HIS ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17420 Z= 0.206 Angle : 0.509 6.185 23746 Z= 0.261 Chirality : 0.044 0.199 2742 Planarity : 0.005 0.078 3022 Dihedral : 7.671 88.216 2556 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 3.45 % Allowed : 18.47 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.46 (0.18), residues: 2110 helix: 0.40 (0.19), residues: 804 sheet: -0.60 (0.32), residues: 270 loop : -0.72 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 772 HIS 0.012 0.001 HIS A 3 PHE 0.024 0.001 PHE A 283 TYR 0.014 0.001 TYR A1049 ARG 0.003 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 321 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7954 (t0) cc_final: 0.7700 (t0) REVERT: A 285 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.4545 (mp0) REVERT: A 532 MET cc_start: 0.7991 (tpp) cc_final: 0.7719 (mmt) REVERT: A 824 ARG cc_start: 0.7898 (tpp-160) cc_final: 0.7604 (ttt90) REVERT: A 865 ASN cc_start: 0.7830 (m-40) cc_final: 0.7426 (p0) REVERT: A 1055 LEU cc_start: 0.8754 (mt) cc_final: 0.8467 (mt) REVERT: B 116 MET cc_start: 0.8756 (ttp) cc_final: 0.8252 (ttm) REVERT: B 286 ASN cc_start: 0.6721 (t0) cc_final: 0.6339 (t0) REVERT: B 474 TYR cc_start: 0.8195 (t80) cc_final: 0.7862 (t80) REVERT: B 761 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8282 (tp40) REVERT: B 926 MET cc_start: 0.7943 (mpp) cc_final: 0.7672 (mpp) outliers start: 65 outliers final: 48 residues processed: 359 average time/residue: 0.2862 time to fit residues: 155.5979 Evaluate side-chains 357 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 307 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 761 GLN Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 907 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 114 optimal weight: 0.0070 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 339 GLN B 299 GLN B 737 HIS B 761 GLN ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17420 Z= 0.192 Angle : 0.506 6.804 23746 Z= 0.259 Chirality : 0.044 0.198 2742 Planarity : 0.004 0.076 3022 Dihedral : 7.618 88.908 2556 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 3.56 % Allowed : 19.59 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.47 (0.18), residues: 2110 helix: 0.37 (0.19), residues: 810 sheet: -0.58 (0.32), residues: 270 loop : -0.71 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 772 HIS 0.012 0.001 HIS A 3 PHE 0.025 0.001 PHE A 283 TYR 0.014 0.001 TYR A1049 ARG 0.004 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 316 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7940 (t0) cc_final: 0.7692 (t0) REVERT: A 285 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.4518 (mp0) REVERT: A 532 MET cc_start: 0.7991 (tpp) cc_final: 0.7736 (mmt) REVERT: A 578 ASN cc_start: 0.6770 (t0) cc_final: 0.6479 (t0) REVERT: A 593 GLU cc_start: 0.5179 (OUTLIER) cc_final: 0.4727 (pm20) REVERT: A 824 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.7596 (ttt90) REVERT: A 865 ASN cc_start: 0.7820 (m-40) cc_final: 0.7414 (p0) REVERT: A 1055 LEU cc_start: 0.8677 (mt) cc_final: 0.8475 (mt) REVERT: B 116 MET cc_start: 0.8788 (ttp) cc_final: 0.8463 (ttp) REVERT: B 270 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7268 (mm-40) REVERT: B 286 ASN cc_start: 0.6717 (t0) cc_final: 0.6336 (t0) REVERT: B 474 TYR cc_start: 0.8207 (t80) cc_final: 0.7877 (t80) REVERT: B 626 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5852 (mt-10) REVERT: B 739 ASN cc_start: 0.6343 (m110) cc_final: 0.6139 (m-40) REVERT: B 761 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8388 (tp40) outliers start: 67 outliers final: 51 residues processed: 355 average time/residue: 0.3006 time to fit residues: 159.1428 Evaluate side-chains 365 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 310 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 761 GLN Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 907 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 299 GLN B 737 HIS B 761 GLN ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17420 Z= 0.244 Angle : 0.544 11.164 23746 Z= 0.277 Chirality : 0.045 0.200 2742 Planarity : 0.005 0.074 3022 Dihedral : 7.736 88.667 2556 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.79 % Favored : 96.16 % Rotamer: Outliers : 4.03 % Allowed : 19.48 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.54 (0.18), residues: 2110 helix: 0.29 (0.19), residues: 804 sheet: -0.61 (0.32), residues: 270 loop : -0.73 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 2 HIS 0.012 0.001 HIS A 3 PHE 0.009 0.001 PHE A 283 TYR 0.017 0.001 TYR A1049 ARG 0.005 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 314 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7959 (t0) cc_final: 0.7697 (t0) REVERT: A 285 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.4743 (mp0) REVERT: A 532 MET cc_start: 0.8065 (tpp) cc_final: 0.7793 (mmt) REVERT: A 578 ASN cc_start: 0.6695 (t0) cc_final: 0.6422 (t0) REVERT: A 593 GLU cc_start: 0.5176 (OUTLIER) cc_final: 0.4680 (pm20) REVERT: A 824 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7609 (ttt90) REVERT: A 865 ASN cc_start: 0.7768 (m-40) cc_final: 0.7393 (p0) REVERT: A 1055 LEU cc_start: 0.8721 (mt) cc_final: 0.8462 (mt) REVERT: B 116 MET cc_start: 0.8761 (ttp) cc_final: 0.8394 (ttp) REVERT: B 286 ASN cc_start: 0.6735 (t0) cc_final: 0.6340 (t0) REVERT: B 474 TYR cc_start: 0.8165 (t80) cc_final: 0.7858 (t80) REVERT: B 626 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5902 (mt-10) REVERT: B 719 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.8038 (p) REVERT: B 739 ASN cc_start: 0.6314 (m110) cc_final: 0.6057 (m-40) REVERT: B 761 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8336 (tp40) outliers start: 76 outliers final: 57 residues processed: 359 average time/residue: 0.2920 time to fit residues: 157.2303 Evaluate side-chains 374 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 312 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 761 GLN Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 907 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 82 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 178 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 299 GLN B 737 HIS B 761 GLN ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17420 Z= 0.189 Angle : 0.518 10.343 23746 Z= 0.263 Chirality : 0.044 0.198 2742 Planarity : 0.004 0.073 3022 Dihedral : 7.608 88.058 2556 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 3.34 % Allowed : 20.44 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.47 (0.18), residues: 2110 helix: 0.34 (0.19), residues: 818 sheet: -0.59 (0.32), residues: 270 loop : -0.67 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 772 HIS 0.012 0.001 HIS A 3 PHE 0.032 0.001 PHE A 154 TYR 0.014 0.001 TYR A 38 ARG 0.006 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 322 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7932 (t0) cc_final: 0.7686 (t0) REVERT: A 285 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.4508 (mp0) REVERT: A 532 MET cc_start: 0.8055 (tpp) cc_final: 0.7811 (mmt) REVERT: A 578 ASN cc_start: 0.6791 (t0) cc_final: 0.6524 (t0) REVERT: A 593 GLU cc_start: 0.5197 (OUTLIER) cc_final: 0.4752 (pm20) REVERT: A 824 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7597 (ttt90) REVERT: A 840 MET cc_start: 0.7907 (mmm) cc_final: 0.7124 (mtp) REVERT: A 865 ASN cc_start: 0.7796 (m-40) cc_final: 0.7413 (p0) REVERT: A 1055 LEU cc_start: 0.8714 (mt) cc_final: 0.8491 (mt) REVERT: B 116 MET cc_start: 0.8772 (ttp) cc_final: 0.7967 (ttp) REVERT: B 286 ASN cc_start: 0.6717 (t0) cc_final: 0.6326 (t0) REVERT: B 474 TYR cc_start: 0.8170 (t80) cc_final: 0.7862 (t80) REVERT: B 626 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5832 (mt-10) REVERT: B 719 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7988 (p) outliers start: 63 outliers final: 50 residues processed: 357 average time/residue: 0.2943 time to fit residues: 158.3472 Evaluate side-chains 369 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 315 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 907 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 299 GLN B 737 HIS B 761 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17420 Z= 0.329 Angle : 0.612 11.359 23746 Z= 0.311 Chirality : 0.047 0.214 2742 Planarity : 0.005 0.070 3022 Dihedral : 8.060 85.732 2556 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 3.50 % Allowed : 20.22 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.81 (0.18), residues: 2110 helix: 0.03 (0.18), residues: 828 sheet: -0.71 (0.32), residues: 270 loop : -0.89 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 2 HIS 0.013 0.001 HIS A 3 PHE 0.029 0.002 PHE A 154 TYR 0.023 0.002 TYR A 878 ARG 0.006 0.000 ARG A 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 310 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7971 (t0) cc_final: 0.7720 (t0) REVERT: A 285 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.4793 (mp0) REVERT: A 532 MET cc_start: 0.8070 (tpp) cc_final: 0.7833 (mmt) REVERT: A 578 ASN cc_start: 0.6785 (t0) cc_final: 0.6522 (t0) REVERT: A 593 GLU cc_start: 0.5270 (OUTLIER) cc_final: 0.4732 (pm20) REVERT: A 824 ARG cc_start: 0.7923 (tpp-160) cc_final: 0.7625 (ttt90) REVERT: A 840 MET cc_start: 0.7899 (mmm) cc_final: 0.7092 (mtp) REVERT: A 855 MET cc_start: 0.7952 (mmt) cc_final: 0.7360 (mmt) REVERT: A 865 ASN cc_start: 0.7772 (m-40) cc_final: 0.7429 (p0) REVERT: A 926 MET cc_start: 0.8259 (mtm) cc_final: 0.7996 (mtm) REVERT: A 1055 LEU cc_start: 0.8756 (mt) cc_final: 0.8510 (mt) REVERT: B 286 ASN cc_start: 0.6690 (t0) cc_final: 0.6268 (t0) REVERT: B 626 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5957 (mt-10) REVERT: B 737 HIS cc_start: 0.7745 (OUTLIER) cc_final: 0.7306 (t70) REVERT: B 739 ASN cc_start: 0.6022 (m-40) cc_final: 0.5395 (t0) outliers start: 66 outliers final: 54 residues processed: 346 average time/residue: 0.2956 time to fit residues: 152.6201 Evaluate side-chains 364 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 306 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 907 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.0270 chunk 51 optimal weight: 0.2980 chunk 153 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 623 GLN B 299 GLN B 737 HIS ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.139430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.129362 restraints weight = 26796.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.131020 restraints weight = 17055.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.132240 restraints weight = 12322.875| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 17420 Z= 0.159 Angle : 0.508 13.448 23746 Z= 0.258 Chirality : 0.043 0.194 2742 Planarity : 0.004 0.069 3022 Dihedral : 7.545 83.975 2556 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 2.76 % Allowed : 20.86 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.46 (0.18), residues: 2110 helix: 0.37 (0.19), residues: 814 sheet: -0.65 (0.32), residues: 270 loop : -0.66 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 772 HIS 0.012 0.001 HIS A 3 PHE 0.010 0.001 PHE B 672 TYR 0.022 0.001 TYR A 878 ARG 0.006 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3824.27 seconds wall clock time: 69 minutes 33.06 seconds (4173.06 seconds total)