Starting phenix.real_space_refine on Sun Dec 10 06:07:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa4_15293/12_2023/8aa4_15293.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa4_15293/12_2023/8aa4_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_15293/12_2023/8aa4_15293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa4_15293/12_2023/8aa4_15293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa4_15293/12_2023/8aa4_15293.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa4_15293/12_2023/8aa4_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-1.21rc1-5172/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: 12.97, per 1000 atoms: 0.95 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: 4.74 Conformation dependent library (CDL) restraints added in 4.4 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: 1.51 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: 5.14 Time building geometry restraints manager: 5.18 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: 2.270 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: 9.960 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 45.420 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.020 ------------------------------------------------------------------------------- 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 : 1.676 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2390 time to fit residues: 25.0605 Evaluate side-chains 55 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2070 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1678 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= 0.312 Angle : 0.587 6.460 18908 Z= 0.327 Chirality : 0.045 0.142 2032 Planarity : 0.004 0.045 2470 Dihedral : 3.986 19.825 1890 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 0.41 % Allowed : 1.77 % Favored : 97.82 % 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: 0.12 (0.20), residues: 1732 helix: -1.06 (0.43), residues: 132 sheet: 1.25 (0.18), residues: 784 loop : -0.93 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 455 HIS 0.005 0.001 HIS B 806 PHE 0.015 0.002 PHE B 527 TYR 0.018 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 : 1.629 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.2441 time to fit residues: 23.9788 Evaluate side-chains 56 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1228 time to fit residues: 2.6116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 107 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 671 GLN A 769 ASN ** A 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN B 417 HIS ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 13928 Z= 0.440 Angle : 0.671 7.615 18908 Z= 0.374 Chirality : 0.048 0.180 2032 Planarity : 0.005 0.064 2470 Dihedral : 4.647 23.070 1890 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 0.41 % Allowed : 2.52 % Favored : 97.07 % 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: -0.41 (0.20), residues: 1732 helix: -1.75 (0.40), residues: 132 sheet: 0.97 (0.18), residues: 770 loop : -1.25 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 455 HIS 0.006 0.002 HIS A 665 PHE 0.014 0.002 PHE A 527 TYR 0.020 0.002 TYR B 265 ARG 0.006 0.001 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 61 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 1.530 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 0.2292 time to fit residues: 21.7142 Evaluate side-chains 56 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1747 time to fit residues: 3.0644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13928 Z= 0.307 Angle : 0.586 7.235 18908 Z= 0.327 Chirality : 0.045 0.153 2032 Planarity : 0.004 0.044 2470 Dihedral : 4.429 21.263 1890 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.57 % Favored : 95.32 % Rotamer: Outliers : 0.07 % Allowed : 3.13 % 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: -0.41 (0.20), residues: 1732 helix: -1.69 (0.40), residues: 132 sheet: 0.93 (0.17), residues: 786 loop : -1.27 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 455 HIS 0.005 0.001 HIS B 806 PHE 0.020 0.002 PHE B 997 TYR 0.019 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 56 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 1.490 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 56 average time/residue: 0.2175 time to fit residues: 20.8025 Evaluate side-chains 56 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1778 time to fit residues: 2.4177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.2980 chunk 150 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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 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: 0.8717 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13928 Z= 0.330 Angle : 0.596 7.427 18908 Z= 0.333 Chirality : 0.046 0.159 2032 Planarity : 0.004 0.048 2470 Dihedral : 4.460 21.187 1890 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.74 % Favored : 95.14 % Rotamer: Outliers : 0.27 % Allowed : 3.54 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1732 helix: -1.73 (0.40), residues: 132 sheet: 0.91 (0.17), residues: 782 loop : -1.35 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 455 HIS 0.005 0.001 HIS B 806 PHE 0.021 0.002 PHE B 997 TYR 0.020 0.002 TYR B 265 ARG 0.004 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: 4 poor density : 56 time to evaluate : 1.463 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 56 average time/residue: 0.2154 time to fit residues: 20.6462 Evaluate side-chains 59 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 1.419 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1627 time to fit residues: 3.1027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 13928 Z= 0.436 Angle : 0.657 7.770 18908 Z= 0.367 Chirality : 0.047 0.180 2032 Planarity : 0.005 0.064 2470 Dihedral : 4.720 22.572 1890 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.97 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % 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: -0.66 (0.20), residues: 1732 helix: -1.86 (0.40), residues: 132 sheet: 0.83 (0.18), residues: 758 loop : -1.44 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 514 HIS 0.007 0.002 HIS A 665 PHE 0.019 0.002 PHE B 997 TYR 0.021 0.002 TYR B 265 ARG 0.005 0.001 ARG B 906 *********************** 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 54 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.626 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2312 time to fit residues: 21.4245 Evaluate side-chains 54 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.480 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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** B 628 GLN B 769 ASN ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13928 Z= 0.173 Angle : 0.514 6.643 18908 Z= 0.286 Chirality : 0.044 0.150 2032 Planarity : 0.003 0.036 2470 Dihedral : 4.198 18.723 1890 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 0.14 % Allowed : 4.90 % Favored : 94.97 % 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: -0.43 (0.20), residues: 1732 helix: -1.50 (0.41), residues: 132 sheet: 0.85 (0.17), residues: 792 loop : -1.26 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 455 HIS 0.005 0.001 HIS B 806 PHE 0.023 0.001 PHE B 997 TYR 0.014 0.001 TYR B 265 ARG 0.002 0.000 ARG A 930 *********************** 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 57 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.625 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 0.2207 time to fit residues: 21.1768 Evaluate side-chains 57 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.480 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1411 time to fit residues: 2.5847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 152 optimal weight: 0.7980 chunk 160 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 ** 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: 0.8711 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13928 Z= 0.303 Angle : 0.574 7.319 18908 Z= 0.320 Chirality : 0.045 0.156 2032 Planarity : 0.004 0.045 2470 Dihedral : 4.373 20.099 1890 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.68 % Favored : 95.20 % Rotamer: Outliers : 0.14 % Allowed : 5.03 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1732 helix: -1.64 (0.40), residues: 132 sheet: 0.83 (0.17), residues: 794 loop : -1.35 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 455 HIS 0.005 0.001 HIS A 665 PHE 0.021 0.002 PHE B 997 TYR 0.020 0.002 TYR B 265 ARG 0.003 0.000 ARG A 302 *********************** 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 57 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.575 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.2250 time to fit residues: 21.1109 Evaluate side-chains 57 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.582 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1678 time to fit residues: 2.8338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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** B 769 ASN ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13928 Z= 0.209 Angle : 0.524 6.804 18908 Z= 0.292 Chirality : 0.044 0.149 2032 Planarity : 0.004 0.036 2470 Dihedral : 4.189 18.986 1890 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.22 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1732 helix: -1.47 (0.41), residues: 132 sheet: 0.89 (0.17), residues: 792 loop : -1.25 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 514 HIS 0.005 0.001 HIS B 806 PHE 0.022 0.001 PHE B 997 TYR 0.016 0.001 TYR B 265 ARG 0.002 0.000 ARG A 302 *********************** 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 54 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.549 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2383 time to fit residues: 21.5212 Evaluate side-chains 54 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 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 537 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13928 Z= 0.291 Angle : 0.566 7.265 18908 Z= 0.316 Chirality : 0.045 0.152 2032 Planarity : 0.004 0.042 2470 Dihedral : 4.340 19.895 1890 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % 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: -0.50 (0.20), residues: 1732 helix: -1.60 (0.40), residues: 132 sheet: 0.81 (0.17), residues: 802 loop : -1.32 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 514 HIS 0.005 0.001 HIS A 665 PHE 0.022 0.002 PHE B 997 TYR 0.019 0.001 TYR B 265 ARG 0.003 0.000 ARG A 302 ********************** 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 54 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.475 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2223 time to fit residues: 20.6554 Evaluate side-chains 54 residues out of total 1468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 141 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.064539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.050554 restraints weight = 89174.778| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.50 r_work: 0.3063 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13928 Z= 0.253 Angle : 0.546 7.133 18908 Z= 0.305 Chirality : 0.044 0.149 2032 Planarity : 0.004 0.037 2470 Dihedral : 4.278 19.669 1890 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.57 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % 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: -0.43 (0.20), residues: 1732 helix: -1.53 (0.41), residues: 132 sheet: 0.84 (0.17), residues: 796 loop : -1.26 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 514 HIS 0.005 0.001 HIS B 806 PHE 0.022 0.001 PHE B 997 TYR 0.018 0.001 TYR B 265 ARG 0.002 0.000 ARG A 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2441.27 seconds wall clock time: 45 minutes 37.31 seconds (2737.31 seconds total)