Starting phenix.real_space_refine on Sat Mar 16 03:46:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa4_15293/03_2024/8aa4_15293.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa4_15293/03_2024/8aa4_15293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa4_15293/03_2024/8aa4_15293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa4_15293/03_2024/8aa4_15293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa4_15293/03_2024/8aa4_15293.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa4_15293/03_2024/8aa4_15293.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8580 2.51 5 N 2330 2.21 5 O 2652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13616 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6808 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 871, 6800 Classifications: {'peptide': 871} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 842} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 871, 6800 Classifications: {'peptide': 871} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 842} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 6944 Chain: "B" Number of atoms: 6808 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 871, 6800 Classifications: {'peptide': 871} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 842} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 871, 6800 Classifications: {'peptide': 871} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 842} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 6944 Time building chain proxies: 13.62, per 1000 atoms: 1.00 Number of scatterers: 13616 At special positions: 0 Unit cell: (144.48, 116.1, 116.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2652 8.00 N 2330 7.00 C 8580 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: 4.93 Conformation dependent library (CDL) restraints added in 5.1 seconds 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 16 sheets defined 11.9% alpha, 46.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.752A pdb=" N ALA A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 149' Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 218 through 223 removed outlier: 6.681A pdb=" N SER A 221 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 222 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 223' Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 411 through 419 Processing helix chain 'A' and resid 706 through 710 Processing helix chain 'A' and resid 799 through 806 Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 888 through 892 Processing helix chain 'A' and resid 919 through 921 No H-bonds generated for 'chain 'A' and resid 919 through 921' Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.752A pdb=" N ALA B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 149' Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 218 through 223 removed outlier: 6.681A pdb=" N SER B 221 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 222 " --> pdb=" O TYR B 219 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 223 " --> pdb=" O GLY B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 223' Processing helix chain 'B' and resid 261 through 276 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 411 through 419 Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 799 through 806 Processing helix chain 'B' and resid 874 through 879 Processing helix chain 'B' and resid 888 through 892 Processing helix chain 'B' and resid 919 through 921 No H-bonds generated for 'chain 'B' and resid 919 through 921' Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.559A pdb=" N ARG A 206 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 184 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE A 230 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 186 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER A 232 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AA4, first strand: chain 'A' and resid 588 through 590 removed outlier: 4.053A pdb=" N ASP A 615 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 734 " --> pdb=" O SER A 686 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLY A 722 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 700 " --> pdb=" O ASN A 720 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN A 720 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS A 702 " --> pdb=" O PHE A 718 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N PHE A 718 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS A 723 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 758 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU A 857 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU A 936 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER A 859 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 934 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 861 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR A 928 " --> pdb=" O ILE A 965 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 965 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ARG A 930 " --> pdb=" O ALA A 963 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA A 963 " --> pdb=" O ARG A 930 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS A 932 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 952 " --> pdb=" O ASN A 998 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 956 " --> pdb=" O GLY A 994 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 990 " --> pdb=" O GLU A 960 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL A 962 " --> pdb=" O SER A 988 " (cutoff:3.500A) removed outlier: 11.187A pdb=" N SER A 988 " --> pdb=" O VAL A 962 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ALA A 239 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLY A 316 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 305 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A 322 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A 346 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN A 339 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 353 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 420 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP A 514 " --> pdb=" O TYR A 486 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 508 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 519 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 547 " --> pdb=" O TYR A 519 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 543 " --> pdb=" O GLN A 523 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 638 through 645 Processing sheet with id=AA6, first strand: chain 'A' and resid 766 through 771 removed outlier: 6.926A pdb=" N PHE A 767 " --> pdb=" O MET A 778 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N MET A 778 " --> pdb=" O PHE A 767 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN A 769 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL A 776 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 787 " --> pdb=" O MET A 778 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 793 through 796 removed outlier: 6.511A pdb=" N ARG A 818 " --> pdb=" O ASP A 794 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 923 through 925 removed outlier: 8.591A pdb=" N ASP A 981 " --> pdb=" O LYS A 869 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR A 871 " --> pdb=" O ASP A 981 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.560A pdb=" N ARG B 206 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 184 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 230 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 186 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER B 232 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 159 Processing sheet with id=AB3, first strand: chain 'B' and resid 588 through 590 removed outlier: 4.053A pdb=" N ASP B 615 " --> pdb=" O SER B 679 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 734 " --> pdb=" O SER B 686 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLY B 722 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 700 " --> pdb=" O ASN B 720 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN B 720 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS B 702 " --> pdb=" O PHE B 718 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE B 718 " --> pdb=" O LYS B 702 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS B 723 " --> pdb=" O LEU B 758 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 758 " --> pdb=" O LYS B 723 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU B 857 " --> pdb=" O LEU B 936 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU B 936 " --> pdb=" O GLU B 857 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER B 859 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE B 934 " --> pdb=" O SER B 859 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE B 861 " --> pdb=" O LYS B 932 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR B 928 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 965 " --> pdb=" O TYR B 928 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ARG B 930 " --> pdb=" O ALA B 963 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA B 963 " --> pdb=" O ARG B 930 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS B 932 " --> pdb=" O ASN B 961 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 952 " --> pdb=" O ASN B 998 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 956 " --> pdb=" O GLY B 994 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 990 " --> pdb=" O GLU B 960 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL B 962 " --> pdb=" O SER B 988 " (cutoff:3.500A) removed outlier: 11.188A pdb=" N SER B 988 " --> pdb=" O VAL B 962 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ALA B 239 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLY B 316 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B 305 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 322 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B 346 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN B 339 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 353 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 420 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP B 514 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 508 " --> pdb=" O PHE B 492 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR B 519 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 547 " --> pdb=" O TYR B 519 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 543 " --> pdb=" O GLN B 523 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 638 through 645 Processing sheet with id=AB5, first strand: chain 'B' and resid 766 through 771 removed outlier: 6.926A pdb=" N PHE B 767 " --> pdb=" O MET B 778 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET B 778 " --> pdb=" O PHE B 767 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN B 769 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL B 776 " --> pdb=" O TYR B 789 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 787 " --> pdb=" O MET B 778 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 793 through 796 removed outlier: 6.511A pdb=" N ARG B 818 " --> pdb=" O ASP B 794 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 923 through 925 removed outlier: 8.591A pdb=" N ASP B 981 " --> pdb=" O LYS B 869 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR B 871 " --> pdb=" O ASP B 981 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1918 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: 5.49 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4488 1.34 - 1.46: 3205 1.46 - 1.58: 6131 1.58 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 13928 Sorted by residual: bond pdb=" N MET B 528 " pdb=" CA MET B 528 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.46e+00 bond pdb=" N MET A 528 " pdb=" CA MET A 528 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.41e+00 bond pdb=" C VAL A 256 " pdb=" O VAL A 256 " ideal model delta sigma weight residual 1.232 1.239 -0.007 8.90e-03 1.26e+04 6.28e-01 bond pdb=" C VAL B 256 " pdb=" O VAL B 256 " ideal model delta sigma weight residual 1.232 1.239 -0.007 8.90e-03 1.26e+04 5.89e-01 bond pdb=" N GLY B 449 " pdb=" CA GLY B 449 " ideal model delta sigma weight residual 1.454 1.448 0.007 9.90e-03 1.02e+04 4.67e-01 ... (remaining 13923 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.41: 406 107.41 - 114.07: 7645 114.07 - 120.72: 5209 120.72 - 127.37: 5506 127.37 - 134.02: 142 Bond angle restraints: 18908 Sorted by residual: angle pdb=" C MET B 528 " pdb=" CA MET B 528 " pdb=" CB MET B 528 " ideal model delta sigma weight residual 110.42 115.85 -5.43 1.99e+00 2.53e-01 7.45e+00 angle pdb=" C MET A 528 " pdb=" CA MET A 528 " pdb=" CB MET A 528 " ideal model delta sigma weight residual 110.42 115.81 -5.39 1.99e+00 2.53e-01 7.34e+00 angle pdb=" C ASN A 525 " pdb=" N ILE A 526 " pdb=" CA ILE A 526 " ideal model delta sigma weight residual 121.97 125.88 -3.91 1.80e+00 3.09e-01 4.71e+00 angle pdb=" C ASN B 525 " pdb=" N ILE B 526 " pdb=" CA ILE B 526 " ideal model delta sigma weight residual 121.97 125.87 -3.90 1.80e+00 3.09e-01 4.69e+00 angle pdb=" C ILE A 526 " pdb=" N PHE A 527 " pdb=" CA PHE A 527 " ideal model delta sigma weight residual 121.54 125.58 -4.04 1.91e+00 2.74e-01 4.47e+00 ... (remaining 18903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.47: 7838 14.47 - 28.95: 258 28.95 - 43.42: 44 43.42 - 57.90: 2 57.90 - 72.37: 2 Dihedral angle restraints: 8144 sinusoidal: 3146 harmonic: 4998 Sorted by residual: dihedral pdb=" CA LEU A 329 " pdb=" CB LEU A 329 " pdb=" CG LEU A 329 " pdb=" CD1 LEU A 329 " ideal model delta sinusoidal sigma weight residual 180.00 134.30 45.70 3 1.50e+01 4.44e-03 8.21e+00 dihedral pdb=" CA LEU B 329 " pdb=" CB LEU B 329 " pdb=" CG LEU B 329 " pdb=" CD1 LEU B 329 " ideal model delta sinusoidal sigma weight residual 180.00 134.32 45.68 3 1.50e+01 4.44e-03 8.21e+00 dihedral pdb=" CA VAL B 335 " pdb=" C VAL B 335 " pdb=" N LYS B 336 " pdb=" CA LYS B 336 " ideal model delta harmonic sigma weight residual 180.00 -166.15 -13.85 0 5.00e+00 4.00e-02 7.68e+00 ... (remaining 8141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1253 0.028 - 0.056: 509 0.056 - 0.084: 110 0.084 - 0.112: 116 0.112 - 0.140: 44 Chirality restraints: 2032 Sorted by residual: chirality pdb=" CA ILE B 736 " pdb=" N ILE B 736 " pdb=" C ILE B 736 " pdb=" CB ILE B 736 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE A 736 " pdb=" N ILE A 736 " pdb=" C ILE A 736 " pdb=" CB ILE A 736 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE B 955 " pdb=" N ILE B 955 " pdb=" C ILE B 955 " pdb=" CB ILE B 955 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 2029 not shown) Planarity restraints: 2470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 783 " -0.015 5.00e-02 4.00e+02 2.32e-02 8.62e-01 pdb=" N PRO A 784 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 784 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 784 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 783 " 0.015 5.00e-02 4.00e+02 2.31e-02 8.52e-01 pdb=" N PRO B 784 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 784 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 784 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 190 " 0.014 5.00e-02 4.00e+02 2.14e-02 7.35e-01 pdb=" N PRO A 191 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " 0.012 5.00e-02 4.00e+02 ... (remaining 2467 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2151 2.77 - 3.30: 11727 3.30 - 3.84: 20743 3.84 - 4.37: 23542 4.37 - 4.90: 45403 Nonbonded interactions: 103566 Sorted by model distance: nonbonded pdb=" OH TYR A 283 " pdb=" OH TYR A 406 " model vdw 2.240 2.440 nonbonded pdb=" OH TYR B 283 " pdb=" OH TYR B 406 " model vdw 2.240 2.440 nonbonded pdb=" OG1 THR B 571 " pdb=" OG SER B 595 " model vdw 2.253 2.440 nonbonded pdb=" OG1 THR A 571 " pdb=" OG SER A 595 " model vdw 2.253 2.440 nonbonded pdb=" OD1 ASP B 550 " pdb=" OH TYR B 633 " model vdw 2.276 2.440 ... (remaining 103561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 112 through 427 or resid 429 through 999)) selection = (chain 'B' and (resid 112 through 427 or resid 429 through 999)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.860 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: 14.380 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 48.630 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 : 0.001 0.017 13928 Z= 0.084 Angle : 0.407 5.433 18908 Z= 0.225 Chirality : 0.041 0.140 2032 Planarity : 0.002 0.023 2470 Dihedral : 7.457 72.370 4968 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.66 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1732 helix: -0.61 (0.47), residues: 142 sheet: 1.37 (0.20), residues: 780 loop : -0.71 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 455 HIS 0.001 0.000 HIS B 665 PHE 0.008 0.001 PHE B 527 TYR 0.006 0.001 TYR A 265 ARG 0.001 0.000 ARG B 302 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.547 Fit side-chains REVERT: B 699 MET cc_start: 0.8600 (ttm) cc_final: 0.8330 (ttp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2194 time to fit residues: 23.4367 Evaluate side-chains 55 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 0.0980 chunk 88 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 52 optimal weight: 0.0970 chunk 82 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 overall best weight: 3.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 490 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN A 665 HIS A 769 ASN ** A 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 HIS B 840 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13928 Z= 0.319 Angle : 0.594 6.552 18908 Z= 0.331 Chirality : 0.046 0.144 2032 Planarity : 0.004 0.045 2470 Dihedral : 4.076 20.269 1890 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 0.41 % Allowed : 1.84 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1732 helix: -1.14 (0.42), residues: 132 sheet: 1.21 (0.18), residues: 780 loop : -0.96 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 284 HIS 0.005 0.001 HIS B 806 PHE 0.015 0.002 PHE B 527 TYR 0.019 0.002 TYR B 265 ARG 0.004 0.001 ARG B 906 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 1.732 Fit side-chains REVERT: B 742 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7576 (t80) outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.2686 time to fit residues: 26.4560 Evaluate side-chains 57 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 742 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN ** A 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN B 417 HIS ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B 769 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13928 Z= 0.213 Angle : 0.526 6.396 18908 Z= 0.292 Chirality : 0.044 0.143 2032 Planarity : 0.003 0.030 2470 Dihedral : 3.965 19.036 1890 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.47 % Rotamer: Outliers : 0.41 % Allowed : 2.11 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1732 helix: -1.25 (0.42), residues: 132 sheet: 1.23 (0.18), residues: 798 loop : -1.01 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 455 HIS 0.005 0.001 HIS B 806 PHE 0.012 0.001 PHE B 527 TYR 0.014 0.001 TYR B 265 ARG 0.002 0.000 ARG B 906 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 1.614 Fit side-chains REVERT: B 699 MET cc_start: 0.8521 (ttm) cc_final: 0.8290 (ttm) REVERT: B 742 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7622 (t80) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.2172 time to fit residues: 21.2499 Evaluate side-chains 58 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 742 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN ** A 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13928 Z= 0.327 Angle : 0.593 7.205 18908 Z= 0.332 Chirality : 0.045 0.149 2032 Planarity : 0.004 0.048 2470 Dihedral : 4.333 21.250 1890 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 0.48 % Allowed : 2.72 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1732 helix: -1.56 (0.41), residues: 132 sheet: 1.04 (0.18), residues: 788 loop : -1.15 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 455 HIS 0.005 0.001 HIS B 806 PHE 0.013 0.002 PHE A 527 TYR 0.020 0.002 TYR B 265 ARG 0.004 0.000 ARG B 906 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 1.369 Fit side-chains REVERT: B 742 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7609 (t80) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.2086 time to fit residues: 20.8528 Evaluate side-chains 60 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 742 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13928 Z= 0.258 Angle : 0.550 6.936 18908 Z= 0.307 Chirality : 0.044 0.146 2032 Planarity : 0.004 0.036 2470 Dihedral : 4.222 19.937 1890 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.10 % Favored : 95.78 % Rotamer: Outliers : 0.41 % Allowed : 3.20 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1732 helix: -1.51 (0.41), residues: 132 sheet: 1.00 (0.17), residues: 788 loop : -1.17 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 455 HIS 0.005 0.001 HIS B 806 PHE 0.013 0.001 PHE A 527 TYR 0.017 0.001 TYR B 265 ARG 0.003 0.000 ARG B 906 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.723 Fit side-chains REVERT: B 742 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7596 (t80) outliers start: 6 outliers final: 4 residues processed: 56 average time/residue: 0.2104 time to fit residues: 20.1151 Evaluate side-chains 59 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 742 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.1980 chunk 33 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 41 optimal weight: 0.1980 chunk 168 optimal weight: 8.9990 chunk 139 optimal weight: 0.4980 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 88 optimal weight: 0.2980 chunk 162 optimal weight: 8.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 HIS ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 13928 Z= 0.146 Angle : 0.483 6.105 18908 Z= 0.269 Chirality : 0.043 0.144 2032 Planarity : 0.003 0.033 2470 Dihedral : 3.896 16.756 1890 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 0.34 % Allowed : 3.88 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1732 helix: -1.20 (0.42), residues: 132 sheet: 1.06 (0.17), residues: 812 loop : -1.07 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 455 HIS 0.004 0.001 HIS B 806 PHE 0.014 0.001 PHE A 527 TYR 0.012 0.001 TYR B 265 ARG 0.001 0.000 ARG A 930 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 1.664 Fit side-chains REVERT: B 742 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7591 (t80) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.2375 time to fit residues: 22.6470 Evaluate side-chains 59 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 742 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 104 optimal weight: 0.0070 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13928 Z= 0.185 Angle : 0.501 6.478 18908 Z= 0.280 Chirality : 0.043 0.144 2032 Planarity : 0.003 0.037 2470 Dihedral : 3.945 17.513 1890 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.10 % Favored : 95.78 % Rotamer: Outliers : 0.34 % Allowed : 4.01 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1732 helix: -1.20 (0.42), residues: 132 sheet: 1.15 (0.17), residues: 802 loop : -1.12 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 455 HIS 0.004 0.001 HIS B 806 PHE 0.013 0.001 PHE A 527 TYR 0.016 0.001 TYR B 265 ARG 0.003 0.000 ARG A 805 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 1.671 Fit side-chains REVERT: B 742 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7620 (t80) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.2312 time to fit residues: 21.8849 Evaluate side-chains 59 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 742 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13928 Z= 0.383 Angle : 0.610 7.461 18908 Z= 0.341 Chirality : 0.046 0.161 2032 Planarity : 0.004 0.053 2470 Dihedral : 4.426 21.169 1890 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.80 % Favored : 95.09 % Rotamer: Outliers : 0.41 % Allowed : 4.08 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 1732 helix: -1.60 (0.40), residues: 132 sheet: 0.91 (0.17), residues: 786 loop : -1.22 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 455 HIS 0.006 0.001 HIS A 665 PHE 0.012 0.002 PHE B 844 TYR 0.020 0.002 TYR B 265 ARG 0.004 0.000 ARG B 906 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.677 Fit side-chains REVERT: B 742 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7648 (t80) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.2122 time to fit residues: 20.6370 Evaluate side-chains 60 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 742 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 122 optimal weight: 0.0870 chunk 47 optimal weight: 0.0060 chunk 141 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 ASN B 769 ASN B 806 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 13928 Z= 0.116 Angle : 0.466 5.776 18908 Z= 0.258 Chirality : 0.043 0.146 2032 Planarity : 0.003 0.031 2470 Dihedral : 3.837 16.149 1890 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.71 % Rotamer: Outliers : 0.20 % Allowed : 4.42 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1732 helix: -1.06 (0.43), residues: 132 sheet: 1.13 (0.17), residues: 798 loop : -1.07 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 455 HIS 0.005 0.001 HIS B 806 PHE 0.016 0.001 PHE B 527 TYR 0.009 0.001 TYR B 265 ARG 0.002 0.000 ARG A 805 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 1.700 Fit side-chains REVERT: B 742 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7557 (t80) outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 0.2184 time to fit residues: 21.1622 Evaluate side-chains 57 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 742 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 114 optimal weight: 0.3980 chunk 173 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 147 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13928 Z= 0.157 Angle : 0.483 6.277 18908 Z= 0.269 Chirality : 0.043 0.144 2032 Planarity : 0.003 0.037 2470 Dihedral : 3.838 16.171 1890 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.05 % Favored : 95.84 % Rotamer: Outliers : 0.20 % Allowed : 4.49 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1732 helix: -1.02 (0.43), residues: 132 sheet: 1.16 (0.17), residues: 802 loop : -1.10 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 455 HIS 0.003 0.001 HIS A 665 PHE 0.014 0.001 PHE B 527 TYR 0.014 0.001 TYR B 265 ARG 0.003 0.000 ARG A 805 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.629 Fit side-chains REVERT: B 742 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7572 (t80) outliers start: 3 outliers final: 2 residues processed: 56 average time/residue: 0.2169 time to fit residues: 20.5582 Evaluate side-chains 57 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 742 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.0770 chunk 127 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 17 optimal weight: 0.0670 chunk 25 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.066332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.052266 restraints weight = 88303.322| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.51 r_work: 0.3110 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13928 Z= 0.153 Angle : 0.480 6.181 18908 Z= 0.267 Chirality : 0.043 0.143 2032 Planarity : 0.003 0.036 2470 Dihedral : 3.825 16.472 1890 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.58 % Favored : 96.30 % Rotamer: Outliers : 0.27 % Allowed : 4.49 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 1732 helix: -0.93 (0.43), residues: 132 sheet: 1.16 (0.17), residues: 802 loop : -1.09 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 455 HIS 0.003 0.001 HIS A 665 PHE 0.014 0.001 PHE B 527 TYR 0.013 0.001 TYR B 265 ARG 0.003 0.000 ARG A 805 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.44 seconds wall clock time: 46 minutes 28.36 seconds (2788.36 seconds total)