Starting phenix.real_space_refine on Thu Sep 18 10:24:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b40_7046/09_2025/6b40_7046.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b40_7046/09_2025/6b40_7046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6b40_7046/09_2025/6b40_7046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b40_7046/09_2025/6b40_7046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6b40_7046/09_2025/6b40_7046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b40_7046/09_2025/6b40_7046.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 100 5.49 5 S 114 5.16 5 C 9836 2.51 5 N 2864 2.21 5 O 3284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16202 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4220 Classifications: {'peptide': 534} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 509} Chain breaks: 1 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "C" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "M" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2759 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 340} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2020 SG CYS A 830 96.024 82.686 61.107 1.00 50.00 S ATOM 2041 SG CYS A 833 97.219 85.622 63.893 1.00 50.00 S Restraints were copied for chains: E, F, G, H, N Time building chain proxies: 5.77, per 1000 atoms: 0.36 Number of scatterers: 16202 At special positions: 0 Unit cell: (155.25, 110.7, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 114 16.00 P 100 15.00 O 3284 8.00 N 2864 7.00 C 9836 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 - 3.00 Amino acid : True - 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 Links applied TRANS " UNK A1107 " - " ALA A1106 " " UNK E1107 " - " ALA E1106 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 750.8 milliseconds Enol-peptide restraints added in 1.4 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A1040 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A1035 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 830 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 833 " pdb=" ZN E1202 " pdb="ZN ZN E1202 " - pdb=" NE2 HIS E1040 " pdb="ZN ZN E1202 " - pdb=" NE2 HIS E1035 " pdb="ZN ZN E1202 " - pdb=" SG CYS E 830 " pdb="ZN ZN E1202 " - pdb=" SG CYS E 833 " Number of angles added : 4 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3436 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 20 sheets defined 24.7% alpha, 9.9% beta 40 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.650A pdb=" N LEU A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 576 Processing helix chain 'A' and resid 583 through 592 removed outlier: 3.975A pdb=" N ALA A 589 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 670 removed outlier: 3.669A pdb=" N THR A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 670 " --> pdb=" O THR A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 676 Processing helix chain 'A' and resid 773 through 785 removed outlier: 3.958A pdb=" N ILE A 777 " --> pdb=" O CYS A 773 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 783 " --> pdb=" O CYS A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 818 removed outlier: 3.566A pdb=" N ARG A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 817 " --> pdb=" O LYS A 813 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS A 818 " --> pdb=" O TRP A 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 812 through 818' Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.726A pdb=" N THR A 859 " --> pdb=" O LYS A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 894 No H-bonds generated for 'chain 'A' and resid 892 through 894' Processing helix chain 'A' and resid 895 through 912 removed outlier: 3.915A pdb=" N SER A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 940 Processing helix chain 'A' and resid 951 through 958 removed outlier: 3.768A pdb=" N GLU A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 958 " --> pdb=" O TYR A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 990 removed outlier: 3.605A pdb=" N LYS A 977 " --> pdb=" O LYS A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1025 removed outlier: 5.364A pdb=" N LYS A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA A1012 " --> pdb=" O ARG A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1047 Processing helix chain 'A' and resid 1060 through 1072 removed outlier: 3.704A pdb=" N GLN A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1096 removed outlier: 3.625A pdb=" N ARG A1087 " --> pdb=" O TYR A1083 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A1092 " --> pdb=" O ASP A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1103 Processing helix chain 'A' and resid 1113 through 1117 removed outlier: 3.859A pdb=" N UNK A1117 " --> pdb=" O UNK A1114 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 560 removed outlier: 3.649A pdb=" N LEU E 557 " --> pdb=" O LEU E 553 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP E 558 " --> pdb=" O GLY E 554 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET E 559 " --> pdb=" O MET E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 576 Processing helix chain 'E' and resid 583 through 592 removed outlier: 3.976A pdb=" N ALA E 589 " --> pdb=" O LYS E 585 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE E 590 " --> pdb=" O GLN E 586 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS E 592 " --> pdb=" O ASP E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 658 through 670 removed outlier: 3.668A pdb=" N THR E 666 " --> pdb=" O ALA E 662 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 670 " --> pdb=" O THR E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 676 Processing helix chain 'E' and resid 773 through 785 removed outlier: 3.958A pdb=" N ILE E 777 " --> pdb=" O CYS E 773 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU E 783 " --> pdb=" O CYS E 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 812 through 818 removed outlier: 3.566A pdb=" N ARG E 816 " --> pdb=" O GLU E 812 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA E 817 " --> pdb=" O LYS E 813 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS E 818 " --> pdb=" O TRP E 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 812 through 818' Processing helix chain 'E' and resid 853 through 861 removed outlier: 3.726A pdb=" N THR E 859 " --> pdb=" O LYS E 855 " (cutoff:3.500A) Processing helix chain 'E' and resid 892 through 894 No H-bonds generated for 'chain 'E' and resid 892 through 894' Processing helix chain 'E' and resid 895 through 912 removed outlier: 3.915A pdb=" N SER E 905 " --> pdb=" O ASN E 901 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 912 " --> pdb=" O VAL E 908 " (cutoff:3.500A) Processing helix chain 'E' and resid 923 through 940 Processing helix chain 'E' and resid 951 through 958 removed outlier: 3.768A pdb=" N GLU E 957 " --> pdb=" O ASN E 953 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU E 958 " --> pdb=" O TYR E 954 " (cutoff:3.500A) Processing helix chain 'E' and resid 973 through 990 removed outlier: 3.606A pdb=" N LYS E 977 " --> pdb=" O LYS E 973 " (cutoff:3.500A) Processing helix chain 'E' and resid 1003 through 1025 removed outlier: 5.364A pdb=" N LYS E1011 " --> pdb=" O VAL E1007 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA E1012 " --> pdb=" O ARG E1008 " (cutoff:3.500A) Processing helix chain 'E' and resid 1041 through 1047 Processing helix chain 'E' and resid 1060 through 1072 removed outlier: 3.703A pdb=" N GLN E1071 " --> pdb=" O LYS E1067 " (cutoff:3.500A) Processing helix chain 'E' and resid 1081 through 1096 removed outlier: 3.625A pdb=" N ARG E1087 " --> pdb=" O TYR E1083 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP E1088 " --> pdb=" O ASN E1084 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR E1092 " --> pdb=" O ASP E1088 " (cutoff:3.500A) Processing helix chain 'E' and resid 1098 through 1103 Processing helix chain 'E' and resid 1113 through 1117 removed outlier: 3.860A pdb=" N UNK E1117 " --> pdb=" O UNK E1114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 635 through 636 removed outlier: 6.371A pdb=" N PHE A 726 " --> pdb=" O PRO A 756 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 720 " --> pdb=" O GLY A 762 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE A 724 " --> pdb=" O ASP A 701 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASP A 701 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N PHE A 726 " --> pdb=" O GLY A 699 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLY A 699 " --> pdb=" O PHE A 726 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL A 728 " --> pdb=" O LYS A 697 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS A 697 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 692 through 693 removed outlier: 7.023A pdb=" N ILE A 692 " --> pdb=" O TYR A 802 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A 799 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 803 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 787 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 31 through 34 removed outlier: 4.405A pdb=" N THR M 31 " --> pdb=" O PHE M 52 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE M 52 " --> pdb=" O THR M 31 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'M' and resid 67 through 68 removed outlier: 3.688A pdb=" N ASP M 67 " --> pdb=" O SER M 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER M 74 " --> pdb=" O ASP M 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'M' and resid 106 through 112 removed outlier: 4.003A pdb=" N LEU M 127 " --> pdb=" O LEU M 146 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR M 133 " --> pdb=" O THR M 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 200 through 202 removed outlier: 3.538A pdb=" N ASP M 202 " --> pdb=" O ARG M 207 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG M 207 " --> pdb=" O ASP M 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 234 through 235 removed outlier: 3.836A pdb=" N SER M 253 " --> pdb=" O ILE M 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE M 271 " --> pdb=" O VAL M 252 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR M 269 " --> pdb=" O ASP M 254 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL M 256 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR M 267 " --> pdb=" O VAL M 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 288 through 289 removed outlier: 3.596A pdb=" N VAL M 295 " --> pdb=" O ALA M 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 318 through 320 removed outlier: 3.713A pdb=" N VAL M 318 " --> pdb=" O HIS M 329 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL M 327 " --> pdb=" O ASN M 320 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 635 through 636 removed outlier: 6.370A pdb=" N PHE E 726 " --> pdb=" O PRO E 756 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS E 720 " --> pdb=" O GLY E 762 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE E 724 " --> pdb=" O ASP E 701 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASP E 701 " --> pdb=" O PHE E 724 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N PHE E 726 " --> pdb=" O GLY E 699 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLY E 699 " --> pdb=" O PHE E 726 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL E 728 " --> pdb=" O LYS E 697 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS E 697 " --> pdb=" O VAL E 728 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 692 through 693 removed outlier: 7.023A pdb=" N ILE E 692 " --> pdb=" O TYR E 802 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG E 799 " --> pdb=" O VAL E 791 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 803 " --> pdb=" O LYS E 787 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS E 787 " --> pdb=" O LEU E 803 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 31 through 34 removed outlier: 4.405A pdb=" N THR N 31 " --> pdb=" O PHE N 52 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE N 52 " --> pdb=" O THR N 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 54 through 55 Processing sheet with id=AB6, first strand: chain 'N' and resid 67 through 68 removed outlier: 3.688A pdb=" N ASP N 67 " --> pdb=" O SER N 74 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER N 74 " --> pdb=" O ASP N 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 106 through 112 removed outlier: 4.003A pdb=" N LEU N 127 " --> pdb=" O LEU N 146 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR N 133 " --> pdb=" O THR N 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 200 through 202 removed outlier: 3.538A pdb=" N ASP N 202 " --> pdb=" O ARG N 207 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG N 207 " --> pdb=" O ASP N 202 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 234 through 235 removed outlier: 3.835A pdb=" N SER N 253 " --> pdb=" O ILE N 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE N 271 " --> pdb=" O VAL N 252 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR N 269 " --> pdb=" O ASP N 254 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL N 256 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR N 267 " --> pdb=" O VAL N 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 288 through 289 removed outlier: 3.597A pdb=" N VAL N 295 " --> pdb=" O ALA N 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 318 through 320 removed outlier: 3.714A pdb=" N VAL N 318 " --> pdb=" O HIS N 329 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL N 327 " --> pdb=" O ASN N 320 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3765 1.33 - 1.45: 3795 1.45 - 1.57: 8808 1.57 - 1.69: 194 1.69 - 1.81: 172 Bond restraints: 16734 Sorted by residual: bond pdb=" C TYR E 878 " pdb=" N PRO E 879 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.19e+00 bond pdb=" C TYR A 878 " pdb=" N PRO A 879 " ideal model delta sigma weight residual 1.334 1.381 -0.048 2.34e-02 1.83e+03 4.13e+00 bond pdb=" CB ILE M 172 " pdb=" CG2 ILE M 172 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" CB ILE N 172 " pdb=" CG2 ILE N 172 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" C ASP E 684 " pdb=" N PRO E 685 " ideal model delta sigma weight residual 1.340 1.394 -0.054 2.76e-02 1.31e+03 3.83e+00 ... (remaining 16729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 22597 3.29 - 6.57: 437 6.57 - 9.86: 40 9.86 - 13.15: 2 13.15 - 16.43: 4 Bond angle restraints: 23080 Sorted by residual: angle pdb=" C ASN A 747 " pdb=" N PRO A 748 " pdb=" CD PRO A 748 " ideal model delta sigma weight residual 120.60 104.17 16.43 2.20e+00 2.07e-01 5.58e+01 angle pdb=" C ASN E 747 " pdb=" N PRO E 748 " pdb=" CD PRO E 748 " ideal model delta sigma weight residual 120.60 104.18 16.42 2.20e+00 2.07e-01 5.57e+01 angle pdb=" C ASN E 747 " pdb=" N PRO E 748 " pdb=" CA PRO E 748 " ideal model delta sigma weight residual 127.00 140.99 -13.99 2.40e+00 1.74e-01 3.40e+01 angle pdb=" C ASN A 747 " pdb=" N PRO A 748 " pdb=" CA PRO A 748 " ideal model delta sigma weight residual 127.00 140.97 -13.97 2.40e+00 1.74e-01 3.39e+01 angle pdb=" N LEU N 173 " pdb=" CA LEU N 173 " pdb=" C LEU N 173 " ideal model delta sigma weight residual 109.24 116.68 -7.44 1.67e+00 3.59e-01 1.98e+01 ... (remaining 23075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 9430 34.43 - 68.86: 450 68.86 - 103.29: 12 103.29 - 137.72: 0 137.72 - 172.15: 4 Dihedral angle restraints: 9896 sinusoidal: 4572 harmonic: 5324 Sorted by residual: dihedral pdb=" CA THR A 882 " pdb=" C THR A 882 " pdb=" N THR A 883 " pdb=" CA THR A 883 " ideal model delta harmonic sigma weight residual 180.00 -136.00 -44.00 0 5.00e+00 4.00e-02 7.74e+01 dihedral pdb=" CA THR E 882 " pdb=" C THR E 882 " pdb=" N THR E 883 " pdb=" CA THR E 883 " ideal model delta harmonic sigma weight residual 180.00 -136.01 -43.99 0 5.00e+00 4.00e-02 7.74e+01 dihedral pdb=" CA UNK E1119 " pdb=" C UNK E1119 " pdb=" N UNK E1120 " pdb=" CA UNK E1120 " ideal model delta harmonic sigma weight residual 180.00 141.49 38.51 0 5.00e+00 4.00e-02 5.93e+01 ... (remaining 9893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1586 0.046 - 0.091: 729 0.091 - 0.137: 225 0.137 - 0.182: 54 0.182 - 0.228: 18 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CB ILE E 695 " pdb=" CA ILE E 695 " pdb=" CG1 ILE E 695 " pdb=" CG2 ILE E 695 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE N 172 " pdb=" N ILE N 172 " pdb=" C ILE N 172 " pdb=" CB ILE N 172 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE A 695 " pdb=" CA ILE A 695 " pdb=" CG1 ILE A 695 " pdb=" CG2 ILE A 695 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2609 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 747 " -0.048 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO A 748 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 748 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 748 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 747 " -0.048 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO E 748 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 748 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 748 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 135 " 0.047 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO N 136 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO N 136 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 136 " 0.039 5.00e-02 4.00e+02 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3920 2.79 - 3.32: 14738 3.32 - 3.85: 27250 3.85 - 4.37: 29910 4.37 - 4.90: 47521 Nonbonded interactions: 123339 Sorted by model distance: nonbonded pdb=" NZ LYS A 563 " pdb=" OP2 DA G 8 " model vdw 2.269 3.120 nonbonded pdb=" OD2 ASP A 891 " pdb=" OG SER A1059 " model vdw 2.279 3.040 nonbonded pdb=" OD2 ASP E 891 " pdb=" OG SER E1059 " model vdw 2.279 3.040 nonbonded pdb=" OG SER M 284 " pdb=" O GLY M 298 " model vdw 2.281 3.040 nonbonded pdb=" OG SER N 284 " pdb=" O GLY N 298 " model vdw 2.281 3.040 ... (remaining 123334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.340 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 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 : 0.008 0.178 16744 Z= 0.346 Angle : 1.135 16.433 23090 Z= 0.622 Chirality : 0.059 0.228 2612 Planarity : 0.008 0.090 2614 Dihedral : 16.851 172.154 6454 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 18.79 % Favored : 80.98 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.22 (0.15), residues: 1788 helix: -2.65 (0.17), residues: 420 sheet: -2.09 (0.35), residues: 200 loop : -4.36 (0.14), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 334 TYR 0.032 0.003 TYR A 994 PHE 0.024 0.004 PHE A 873 TRP 0.035 0.004 TRP A 917 HIS 0.012 0.003 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00734 (16734) covalent geometry : angle 1.12821 (23080) hydrogen bonds : bond 0.19793 ( 430) hydrogen bonds : angle 7.84012 ( 1140) metal coordination : bond 0.12343 ( 8) metal coordination : angle 9.23063 ( 4) link_TRANS : bond 0.00312 ( 2) link_TRANS : angle 1.09506 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8028 (mt-10) REVERT: A 1034 LEU cc_start: 0.8496 (mp) cc_final: 0.8262 (tt) REVERT: A 1038 ILE cc_start: 0.8978 (pt) cc_final: 0.8582 (pt) REVERT: M 197 TYR cc_start: 0.5294 (m-10) cc_final: 0.5028 (m-10) REVERT: M 234 VAL cc_start: 0.7755 (t) cc_final: 0.7478 (t) REVERT: E 759 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7944 (mt-10) REVERT: E 939 LYS cc_start: 0.8457 (tppt) cc_final: 0.8197 (tppt) REVERT: E 1003 MET cc_start: 0.6726 (mmm) cc_final: 0.4644 (mmm) REVERT: E 1034 LEU cc_start: 0.8471 (mp) cc_final: 0.8251 (tt) REVERT: E 1101 LEU cc_start: 0.9046 (mt) cc_final: 0.8835 (tt) REVERT: N 234 VAL cc_start: 0.7622 (t) cc_final: 0.7276 (t) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.1665 time to fit residues: 92.2921 Evaluate side-chains 212 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 GLN A 915 HIS A1042 GLN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 780 GLN E 792 HIS E 915 HIS E1042 GLN ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.106522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086312 restraints weight = 54013.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.088807 restraints weight = 33883.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.090551 restraints weight = 23996.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.091754 restraints weight = 18686.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.092622 restraints weight = 15540.516| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16744 Z= 0.286 Angle : 0.920 10.066 23090 Z= 0.488 Chirality : 0.049 0.194 2612 Planarity : 0.007 0.069 2614 Dihedral : 21.815 177.677 3050 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 17.67 % Favored : 81.99 % Rotamer: Outliers : 0.19 % Allowed : 2.17 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.49 (0.17), residues: 1788 helix: -0.87 (0.23), residues: 434 sheet: -2.13 (0.35), residues: 194 loop : -4.32 (0.14), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 207 TYR 0.017 0.002 TYR N 241 PHE 0.021 0.002 PHE A 873 TRP 0.023 0.003 TRP A 917 HIS 0.010 0.002 HIS N 161 Details of bonding type rmsd covalent geometry : bond 0.00603 (16734) covalent geometry : angle 0.91907 (23080) hydrogen bonds : bond 0.06090 ( 430) hydrogen bonds : angle 5.71750 ( 1140) metal coordination : bond 0.03040 ( 8) metal coordination : angle 3.53421 ( 4) link_TRANS : bond 0.00152 ( 2) link_TRANS : angle 0.24890 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 263 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.6978 (tmm) cc_final: 0.6701 (tmm) REVERT: A 595 MET cc_start: 0.7452 (mtt) cc_final: 0.7201 (mtt) REVERT: A 711 GLU cc_start: 0.7837 (pt0) cc_final: 0.7561 (tt0) REVERT: A 734 MET cc_start: 0.2130 (ptp) cc_final: 0.1371 (tpt) REVERT: A 759 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8325 (mt-10) REVERT: A 816 ARG cc_start: 0.9041 (mtp85) cc_final: 0.8657 (mtp85) REVERT: A 847 TYR cc_start: 0.7486 (m-80) cc_final: 0.6587 (m-80) REVERT: A 977 LYS cc_start: 0.9219 (tttt) cc_final: 0.9008 (ttmt) REVERT: A 1053 SER cc_start: 0.8659 (p) cc_final: 0.8317 (m) REVERT: M 1 MET cc_start: 0.7450 (tmm) cc_final: 0.7247 (tmm) REVERT: M 197 TYR cc_start: 0.6868 (m-10) cc_final: 0.6617 (m-10) REVERT: M 233 MET cc_start: 0.7908 (tpt) cc_final: 0.7236 (tpt) REVERT: M 274 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7330 (tm-30) REVERT: E 547 MET cc_start: 0.7289 (tmm) cc_final: 0.7006 (tmm) REVERT: E 595 MET cc_start: 0.7430 (mtt) cc_final: 0.7094 (mtt) REVERT: E 734 MET cc_start: 0.1966 (ptp) cc_final: 0.1082 (tpt) REVERT: E 759 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8253 (mt-10) REVERT: E 847 TYR cc_start: 0.7247 (m-80) cc_final: 0.6299 (m-80) REVERT: E 857 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7620 (tm-30) REVERT: E 927 ILE cc_start: 0.9466 (mm) cc_final: 0.9265 (tt) REVERT: E 939 LYS cc_start: 0.9191 (tppt) cc_final: 0.8600 (tptt) REVERT: E 1038 ILE cc_start: 0.9254 (pt) cc_final: 0.8989 (mp) REVERT: N 1 MET cc_start: 0.7431 (tmm) cc_final: 0.7207 (tmm) REVERT: N 95 TRP cc_start: 0.7432 (m-90) cc_final: 0.7141 (m-90) REVERT: N 234 VAL cc_start: 0.8924 (t) cc_final: 0.8490 (p) outliers start: 3 outliers final: 0 residues processed: 265 average time/residue: 0.1536 time to fit residues: 58.5734 Evaluate side-chains 183 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 132 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 139 optimal weight: 0.0970 chunk 137 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 HIS A1042 GLN ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1042 GLN ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 ASN ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.108006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.088113 restraints weight = 55373.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.090856 restraints weight = 33854.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.092734 restraints weight = 23503.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.094044 restraints weight = 17944.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.094966 restraints weight = 14705.478| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16744 Z= 0.197 Angle : 0.791 8.015 23090 Z= 0.427 Chirality : 0.045 0.217 2612 Planarity : 0.006 0.058 2614 Dihedral : 21.409 175.054 3050 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 17.34 % Favored : 82.49 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.11 (0.18), residues: 1788 helix: -0.27 (0.24), residues: 432 sheet: -1.92 (0.35), residues: 200 loop : -4.20 (0.15), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E1102 TYR 0.029 0.002 TYR E 828 PHE 0.016 0.002 PHE M 52 TRP 0.021 0.002 TRP A 917 HIS 0.008 0.001 HIS M 161 Details of bonding type rmsd covalent geometry : bond 0.00426 (16734) covalent geometry : angle 0.79104 (23080) hydrogen bonds : bond 0.05079 ( 430) hydrogen bonds : angle 5.08547 ( 1140) metal coordination : bond 0.01683 ( 8) metal coordination : angle 2.38017 ( 4) link_TRANS : bond 0.00110 ( 2) link_TRANS : angle 0.26324 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 668 GLU cc_start: 0.8865 (tt0) cc_final: 0.8170 (tm-30) REVERT: A 734 MET cc_start: 0.1968 (ptp) cc_final: 0.1446 (tpt) REVERT: A 759 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8203 (mt-10) REVERT: A 816 ARG cc_start: 0.9003 (mtp85) cc_final: 0.8792 (mtp85) REVERT: A 862 LYS cc_start: 0.8609 (tmtt) cc_final: 0.8334 (tptp) REVERT: A 931 GLU cc_start: 0.8905 (tt0) cc_final: 0.8248 (tp30) REVERT: A 977 LYS cc_start: 0.9134 (tttt) cc_final: 0.8899 (ttmt) REVERT: A 1043 GLU cc_start: 0.8573 (pm20) cc_final: 0.8338 (pm20) REVERT: A 1053 SER cc_start: 0.8615 (p) cc_final: 0.8342 (m) REVERT: M 1 MET cc_start: 0.7422 (tmm) cc_final: 0.7158 (tmm) REVERT: M 233 MET cc_start: 0.7660 (tpt) cc_final: 0.6657 (tpt) REVERT: M 274 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7321 (tm-30) REVERT: E 667 LEU cc_start: 0.9124 (mm) cc_final: 0.8880 (mm) REVERT: E 668 GLU cc_start: 0.8811 (tt0) cc_final: 0.8235 (tm-30) REVERT: E 734 MET cc_start: 0.2150 (ptp) cc_final: 0.1830 (tpt) REVERT: E 759 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8217 (mt-10) REVERT: E 857 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7590 (tm-30) REVERT: E 927 ILE cc_start: 0.9434 (mm) cc_final: 0.9231 (tt) REVERT: E 939 LYS cc_start: 0.9147 (tppt) cc_final: 0.8611 (tptt) REVERT: E 1038 ILE cc_start: 0.9237 (pt) cc_final: 0.8928 (mp) REVERT: E 1043 GLU cc_start: 0.8519 (pm20) cc_final: 0.8309 (pm20) REVERT: E 1053 SER cc_start: 0.8653 (p) cc_final: 0.8383 (m) REVERT: N 1 MET cc_start: 0.7360 (tmm) cc_final: 0.7094 (tmm) REVERT: N 234 VAL cc_start: 0.8575 (t) cc_final: 0.8327 (p) REVERT: N 274 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7591 (tm-30) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1359 time to fit residues: 47.5128 Evaluate side-chains 181 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 133 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 136 optimal weight: 0.2980 chunk 172 optimal weight: 10.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1024 HIS ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 ASN ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.110525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.090638 restraints weight = 54555.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.093443 restraints weight = 33070.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.095330 restraints weight = 22792.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.096685 restraints weight = 17358.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.097597 restraints weight = 14155.536| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16744 Z= 0.160 Angle : 0.741 7.490 23090 Z= 0.401 Chirality : 0.044 0.222 2612 Planarity : 0.005 0.061 2614 Dihedral : 21.287 175.591 3050 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.87 (0.18), residues: 1788 helix: 0.02 (0.25), residues: 446 sheet: -1.80 (0.35), residues: 204 loop : -4.12 (0.15), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 909 TYR 0.024 0.002 TYR A 828 PHE 0.013 0.001 PHE A 640 TRP 0.045 0.002 TRP E 917 HIS 0.011 0.001 HIS M 161 Details of bonding type rmsd covalent geometry : bond 0.00352 (16734) covalent geometry : angle 0.74046 (23080) hydrogen bonds : bond 0.04572 ( 430) hydrogen bonds : angle 4.69410 ( 1140) metal coordination : bond 0.01094 ( 8) metal coordination : angle 1.77023 ( 4) link_TRANS : bond 0.00045 ( 2) link_TRANS : angle 0.28273 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 MET cc_start: 0.7526 (ttt) cc_final: 0.7293 (ttt) REVERT: A 668 GLU cc_start: 0.8793 (tt0) cc_final: 0.8258 (tm-30) REVERT: A 734 MET cc_start: 0.2209 (ptp) cc_final: 0.1862 (tpt) REVERT: A 759 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8149 (mt-10) REVERT: A 782 LEU cc_start: 0.9253 (tp) cc_final: 0.9036 (mm) REVERT: A 931 GLU cc_start: 0.8835 (tt0) cc_final: 0.8187 (tp30) REVERT: M 1 MET cc_start: 0.7653 (tmm) cc_final: 0.7239 (tmm) REVERT: M 84 MET cc_start: 0.4820 (mtt) cc_final: 0.4453 (mtt) REVERT: M 233 MET cc_start: 0.8127 (tpt) cc_final: 0.7459 (tpt) REVERT: M 259 LYS cc_start: 0.6261 (pttp) cc_final: 0.5796 (tppt) REVERT: M 273 MET cc_start: 0.8143 (tpp) cc_final: 0.7875 (tpp) REVERT: E 547 MET cc_start: 0.7512 (tmm) cc_final: 0.7276 (tmm) REVERT: E 667 LEU cc_start: 0.9111 (mm) cc_final: 0.8892 (tp) REVERT: E 668 GLU cc_start: 0.8737 (tt0) cc_final: 0.8314 (tm-30) REVERT: E 759 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8134 (mt-10) REVERT: E 782 LEU cc_start: 0.9239 (tp) cc_final: 0.9035 (mm) REVERT: E 816 ARG cc_start: 0.8654 (mtp85) cc_final: 0.8245 (mtp85) REVERT: E 857 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7636 (tm-30) REVERT: E 939 LYS cc_start: 0.8998 (tppt) cc_final: 0.8430 (tppt) REVERT: E 1038 ILE cc_start: 0.9168 (pt) cc_final: 0.8900 (mp) REVERT: E 1053 SER cc_start: 0.8424 (p) cc_final: 0.8213 (m) REVERT: N 1 MET cc_start: 0.7762 (tmm) cc_final: 0.7384 (tmm) REVERT: N 84 MET cc_start: 0.4718 (mtt) cc_final: 0.4400 (mtt) REVERT: N 106 ASP cc_start: 0.7916 (t0) cc_final: 0.7542 (m-30) REVERT: N 233 MET cc_start: 0.7922 (mmm) cc_final: 0.7243 (mmm) REVERT: N 234 VAL cc_start: 0.8699 (t) cc_final: 0.8471 (t) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1375 time to fit residues: 50.7121 Evaluate side-chains 185 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 170 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 HIS A 963 HIS ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 GLN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1042 GLN ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 47 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 ASN ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.102920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.083480 restraints weight = 56279.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085876 restraints weight = 35357.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.087592 restraints weight = 25235.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088774 restraints weight = 19604.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089598 restraints weight = 16302.517| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 16744 Z= 0.317 Angle : 0.927 11.189 23090 Z= 0.492 Chirality : 0.050 0.230 2612 Planarity : 0.007 0.095 2614 Dihedral : 21.732 177.396 3050 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 19.80 % Favored : 79.98 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.02 (0.18), residues: 1788 helix: -0.36 (0.24), residues: 446 sheet: -1.77 (0.34), residues: 216 loop : -4.15 (0.15), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1078 TYR 0.036 0.003 TYR A 828 PHE 0.017 0.002 PHE A 873 TRP 0.043 0.004 TRP E 917 HIS 0.008 0.002 HIS A1076 Details of bonding type rmsd covalent geometry : bond 0.00674 (16734) covalent geometry : angle 0.92426 (23080) hydrogen bonds : bond 0.06032 ( 430) hydrogen bonds : angle 5.49245 ( 1140) metal coordination : bond 0.03670 ( 8) metal coordination : angle 5.23761 ( 4) link_TRANS : bond 0.00206 ( 2) link_TRANS : angle 0.27056 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 668 GLU cc_start: 0.8788 (tt0) cc_final: 0.8231 (tm-30) REVERT: A 734 MET cc_start: 0.2187 (ptp) cc_final: 0.1171 (tpt) REVERT: A 759 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8001 (mt-10) REVERT: M 1 MET cc_start: 0.7576 (tmm) cc_final: 0.7195 (tmm) REVERT: M 233 MET cc_start: 0.7759 (tpt) cc_final: 0.7145 (tpt) REVERT: M 244 HIS cc_start: 0.7301 (m-70) cc_final: 0.7095 (m-70) REVERT: M 259 LYS cc_start: 0.6588 (pttp) cc_final: 0.6310 (tppt) REVERT: E 667 LEU cc_start: 0.9216 (mm) cc_final: 0.8988 (mm) REVERT: E 668 GLU cc_start: 0.8741 (tt0) cc_final: 0.8472 (tm-30) REVERT: E 759 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8092 (mt-10) REVERT: E 816 ARG cc_start: 0.8505 (mtp85) cc_final: 0.7904 (mtp85) REVERT: E 927 ILE cc_start: 0.9406 (mm) cc_final: 0.9192 (tt) REVERT: E 939 LYS cc_start: 0.9171 (tppt) cc_final: 0.8547 (tppt) REVERT: N 1 MET cc_start: 0.7588 (tmm) cc_final: 0.7118 (tmm) REVERT: N 203 MET cc_start: 0.8003 (mpp) cc_final: 0.7235 (mpp) REVERT: N 233 MET cc_start: 0.8425 (mmm) cc_final: 0.7850 (mmm) REVERT: N 234 VAL cc_start: 0.8783 (t) cc_final: 0.8381 (p) REVERT: N 244 HIS cc_start: 0.6950 (m-70) cc_final: 0.6656 (m90) REVERT: N 294 PHE cc_start: 0.7921 (m-80) cc_final: 0.7630 (m-10) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1310 time to fit residues: 41.9849 Evaluate side-chains 171 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1042 GLN N 129 GLN N 340 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.111107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.091494 restraints weight = 54170.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.094229 restraints weight = 33025.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096099 restraints weight = 22873.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.097415 restraints weight = 17493.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098242 restraints weight = 14321.612| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16744 Z= 0.143 Angle : 0.728 7.702 23090 Z= 0.393 Chirality : 0.044 0.186 2612 Planarity : 0.005 0.052 2614 Dihedral : 21.252 172.978 3050 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.16 % Favored : 84.84 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.56 (0.18), residues: 1788 helix: 0.30 (0.24), residues: 446 sheet: -1.09 (0.37), residues: 194 loop : -4.03 (0.15), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 909 TYR 0.023 0.002 TYR A 828 PHE 0.015 0.001 PHE A 640 TRP 0.039 0.002 TRP A 917 HIS 0.007 0.001 HIS E 641 Details of bonding type rmsd covalent geometry : bond 0.00317 (16734) covalent geometry : angle 0.72773 (23080) hydrogen bonds : bond 0.04113 ( 430) hydrogen bonds : angle 4.55200 ( 1140) metal coordination : bond 0.00351 ( 8) metal coordination : angle 1.99388 ( 4) link_TRANS : bond 0.00007 ( 2) link_TRANS : angle 0.33268 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 668 GLU cc_start: 0.8803 (tt0) cc_final: 0.8406 (tm-30) REVERT: A 759 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8011 (mt-10) REVERT: A 816 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8203 (mtp85) REVERT: A 847 TYR cc_start: 0.6360 (m-80) cc_final: 0.6042 (m-80) REVERT: A 909 ARG cc_start: 0.8912 (mmt90) cc_final: 0.8514 (mmt180) REVERT: A 931 GLU cc_start: 0.8767 (tt0) cc_final: 0.8169 (tp30) REVERT: M 1 MET cc_start: 0.7716 (tmm) cc_final: 0.7340 (tmm) REVERT: M 259 LYS cc_start: 0.6406 (pttp) cc_final: 0.5992 (tppt) REVERT: E 667 LEU cc_start: 0.9159 (mm) cc_final: 0.8951 (tp) REVERT: E 759 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8177 (mt-10) REVERT: E 816 ARG cc_start: 0.8615 (mtp85) cc_final: 0.8283 (mtp85) REVERT: E 931 GLU cc_start: 0.8812 (tt0) cc_final: 0.7696 (tm-30) REVERT: E 939 LYS cc_start: 0.9003 (tppt) cc_final: 0.8404 (tppt) REVERT: N 1 MET cc_start: 0.7750 (tmm) cc_final: 0.7289 (tmm) REVERT: N 49 PHE cc_start: 0.6939 (m-10) cc_final: 0.6674 (m-10) REVERT: N 172 ILE cc_start: 0.7324 (mt) cc_final: 0.7108 (mp) REVERT: N 233 MET cc_start: 0.8063 (mmm) cc_final: 0.7316 (tpt) REVERT: N 234 VAL cc_start: 0.8611 (t) cc_final: 0.8375 (p) REVERT: N 294 PHE cc_start: 0.7708 (m-80) cc_final: 0.7342 (m-10) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1294 time to fit residues: 46.0026 Evaluate side-chains 179 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 138 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** 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 = 0.3807 r_free = 0.3807 target = 0.105674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.085836 restraints weight = 54227.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.088474 restraints weight = 33166.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.090321 restraints weight = 23107.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.091584 restraints weight = 17657.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.092476 restraints weight = 14513.038| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16744 Z= 0.233 Angle : 0.809 8.827 23090 Z= 0.432 Chirality : 0.046 0.218 2612 Planarity : 0.006 0.069 2614 Dihedral : 21.379 177.360 3050 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.46 % Favored : 81.54 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.58 (0.18), residues: 1788 helix: 0.29 (0.24), residues: 436 sheet: -1.38 (0.35), residues: 214 loop : -3.99 (0.16), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 909 TYR 0.025 0.002 TYR A 828 PHE 0.014 0.002 PHE M 198 TRP 0.028 0.002 TRP N 208 HIS 0.006 0.001 HIS E 641 Details of bonding type rmsd covalent geometry : bond 0.00504 (16734) covalent geometry : angle 0.80834 (23080) hydrogen bonds : bond 0.04922 ( 430) hydrogen bonds : angle 5.00567 ( 1140) metal coordination : bond 0.02365 ( 8) metal coordination : angle 3.51574 ( 4) link_TRANS : bond 0.00129 ( 2) link_TRANS : angle 0.27031 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 668 GLU cc_start: 0.8788 (tt0) cc_final: 0.8466 (tm-30) REVERT: A 759 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8154 (mt-10) REVERT: A 847 TYR cc_start: 0.6588 (m-80) cc_final: 0.6301 (m-80) REVERT: M 1 MET cc_start: 0.7579 (tmm) cc_final: 0.7185 (tmm) REVERT: M 233 MET cc_start: 0.8189 (tpt) cc_final: 0.7367 (tpt) REVERT: M 259 LYS cc_start: 0.6386 (pttp) cc_final: 0.5968 (tppt) REVERT: E 759 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8265 (mt-10) REVERT: E 857 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7750 (tm-30) REVERT: E 939 LYS cc_start: 0.9132 (tppt) cc_final: 0.8708 (tppt) REVERT: E 995 ARG cc_start: 0.7605 (mmm-85) cc_final: 0.7196 (mmm160) REVERT: N 1 MET cc_start: 0.7407 (tmm) cc_final: 0.7094 (tmm) REVERT: N 49 PHE cc_start: 0.6693 (m-10) cc_final: 0.6470 (m-10) REVERT: N 84 MET cc_start: 0.5401 (mtt) cc_final: 0.5197 (mtt) REVERT: N 203 MET cc_start: 0.7949 (mpp) cc_final: 0.7662 (mpp) REVERT: N 209 ASN cc_start: 0.8557 (m110) cc_final: 0.8316 (m110) REVERT: N 233 MET cc_start: 0.8435 (mmm) cc_final: 0.8040 (mmm) REVERT: N 234 VAL cc_start: 0.8803 (t) cc_final: 0.8362 (p) REVERT: N 294 PHE cc_start: 0.7828 (m-80) cc_final: 0.7496 (m-10) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1205 time to fit residues: 39.2830 Evaluate side-chains 163 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 70 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 161 HIS ** 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 = 0.3907 r_free = 0.3907 target = 0.112129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.092379 restraints weight = 54238.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095176 restraints weight = 33013.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.097069 restraints weight = 22749.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.098388 restraints weight = 17285.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.099222 restraints weight = 14145.378| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16744 Z= 0.137 Angle : 0.716 7.113 23090 Z= 0.385 Chirality : 0.043 0.175 2612 Planarity : 0.005 0.054 2614 Dihedral : 21.052 174.916 3050 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.21 % Favored : 84.79 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.26 (0.19), residues: 1788 helix: 0.80 (0.25), residues: 424 sheet: -0.51 (0.38), residues: 188 loop : -3.93 (0.15), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 909 TYR 0.021 0.001 TYR A 828 PHE 0.018 0.001 PHE M 198 TRP 0.020 0.002 TRP N 208 HIS 0.007 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00305 (16734) covalent geometry : angle 0.71564 (23080) hydrogen bonds : bond 0.03905 ( 430) hydrogen bonds : angle 4.40576 ( 1140) metal coordination : bond 0.00559 ( 8) metal coordination : angle 1.45643 ( 4) link_TRANS : bond 0.00009 ( 2) link_TRANS : angle 0.25630 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 HIS cc_start: 0.6264 (t-90) cc_final: 0.5987 (t-170) REVERT: A 816 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8444 (mtp85) REVERT: A 931 GLU cc_start: 0.8782 (tt0) cc_final: 0.8206 (tp30) REVERT: A 1089 VAL cc_start: 0.8593 (t) cc_final: 0.8370 (t) REVERT: M 1 MET cc_start: 0.7709 (tmm) cc_final: 0.7327 (tmm) REVERT: M 233 MET cc_start: 0.8096 (tpt) cc_final: 0.7748 (tpt) REVERT: E 759 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8317 (mt-10) REVERT: E 931 GLU cc_start: 0.8766 (tt0) cc_final: 0.8133 (tp30) REVERT: E 939 LYS cc_start: 0.9000 (tppt) cc_final: 0.8418 (tppt) REVERT: E 1003 MET cc_start: 0.8070 (ptt) cc_final: 0.7793 (pmm) REVERT: E 1089 VAL cc_start: 0.8591 (t) cc_final: 0.8337 (t) REVERT: N 1 MET cc_start: 0.7699 (tmm) cc_final: 0.7314 (tmm) REVERT: N 49 PHE cc_start: 0.6978 (m-10) cc_final: 0.6611 (m-10) REVERT: N 172 ILE cc_start: 0.6392 (mt) cc_final: 0.6186 (mt) REVERT: N 197 TYR cc_start: 0.6981 (m-10) cc_final: 0.6755 (m-10) REVERT: N 234 VAL cc_start: 0.8710 (t) cc_final: 0.8272 (t) REVERT: N 294 PHE cc_start: 0.7569 (m-80) cc_final: 0.7234 (m-10) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1146 time to fit residues: 40.8302 Evaluate side-chains 177 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 35 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 157 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 161 HIS ** 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 = 0.3814 r_free = 0.3814 target = 0.106142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.086291 restraints weight = 55417.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.088838 restraints weight = 34671.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.090604 restraints weight = 24489.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.091858 restraints weight = 18986.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.092675 restraints weight = 15711.038| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16744 Z= 0.240 Angle : 0.825 9.119 23090 Z= 0.438 Chirality : 0.047 0.299 2612 Planarity : 0.006 0.085 2614 Dihedral : 21.274 177.508 3050 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.34 % Favored : 81.66 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.18), residues: 1788 helix: 0.34 (0.25), residues: 436 sheet: -0.91 (0.36), residues: 210 loop : -4.02 (0.15), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 909 TYR 0.024 0.002 TYR A 828 PHE 0.018 0.002 PHE M 198 TRP 0.031 0.003 TRP M 208 HIS 0.006 0.001 HIS N 340 Details of bonding type rmsd covalent geometry : bond 0.00522 (16734) covalent geometry : angle 0.82305 (23080) hydrogen bonds : bond 0.05016 ( 430) hydrogen bonds : angle 4.92590 ( 1140) metal coordination : bond 0.02463 ( 8) metal coordination : angle 4.30220 ( 4) link_TRANS : bond 0.00133 ( 2) link_TRANS : angle 0.26174 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 HIS cc_start: 0.6554 (t-90) cc_final: 0.6186 (t-170) REVERT: A 809 MET cc_start: 0.7755 (mpp) cc_final: 0.7452 (mpp) REVERT: A 1003 MET cc_start: 0.7682 (mmm) cc_final: 0.7177 (mmp) REVERT: A 1088 ASP cc_start: 0.8332 (p0) cc_final: 0.8106 (m-30) REVERT: M 1 MET cc_start: 0.7662 (tmm) cc_final: 0.7216 (tmm) REVERT: M 233 MET cc_start: 0.8122 (tpt) cc_final: 0.7542 (tpt) REVERT: E 759 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8456 (mt-10) REVERT: E 857 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7688 (tm-30) REVERT: E 939 LYS cc_start: 0.9090 (tppt) cc_final: 0.8656 (tppt) REVERT: N 1 MET cc_start: 0.7722 (tmm) cc_final: 0.7318 (tmm) REVERT: N 84 MET cc_start: 0.5669 (mtt) cc_final: 0.5401 (mtt) REVERT: N 233 MET cc_start: 0.7498 (mmm) cc_final: 0.6780 (mmm) REVERT: N 294 PHE cc_start: 0.7849 (m-80) cc_final: 0.7579 (m-10) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1094 time to fit residues: 36.2280 Evaluate side-chains 165 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 0.0470 chunk 43 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 165 optimal weight: 0.0770 overall best weight: 0.9638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 161 HIS ** 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 = 0.3904 r_free = 0.3904 target = 0.112115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.092235 restraints weight = 53895.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.095012 restraints weight = 32682.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.096981 restraints weight = 22549.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.098335 restraints weight = 17111.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.099237 restraints weight = 13941.656| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16744 Z= 0.140 Angle : 0.730 8.916 23090 Z= 0.390 Chirality : 0.044 0.304 2612 Planarity : 0.005 0.053 2614 Dihedral : 21.002 174.873 3050 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.04 % Favored : 84.96 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.22 (0.19), residues: 1788 helix: 0.78 (0.26), residues: 422 sheet: -0.44 (0.38), residues: 186 loop : -3.88 (0.15), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 909 TYR 0.023 0.002 TYR M 199 PHE 0.017 0.001 PHE M 198 TRP 0.025 0.002 TRP M 208 HIS 0.010 0.001 HIS N 340 Details of bonding type rmsd covalent geometry : bond 0.00315 (16734) covalent geometry : angle 0.73012 (23080) hydrogen bonds : bond 0.03930 ( 430) hydrogen bonds : angle 4.39815 ( 1140) metal coordination : bond 0.00544 ( 8) metal coordination : angle 1.72563 ( 4) link_TRANS : bond 0.00021 ( 2) link_TRANS : angle 0.20781 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 809 MET cc_start: 0.7735 (mpp) cc_final: 0.6968 (mpp) REVERT: A 931 GLU cc_start: 0.8782 (tt0) cc_final: 0.8164 (tp30) REVERT: M 1 MET cc_start: 0.7655 (tmm) cc_final: 0.7255 (tmm) REVERT: M 233 MET cc_start: 0.8072 (tpt) cc_final: 0.7719 (tpt) REVERT: M 273 MET cc_start: 0.7324 (tpp) cc_final: 0.6884 (tpp) REVERT: E 759 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8060 (mt-10) REVERT: E 813 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7875 (ttpt) REVERT: E 931 GLU cc_start: 0.8793 (tt0) cc_final: 0.7840 (tm-30) REVERT: E 939 LYS cc_start: 0.8996 (tppt) cc_final: 0.8392 (tppt) REVERT: E 995 ARG cc_start: 0.7841 (mmm160) cc_final: 0.7563 (mmm160) REVERT: E 1003 MET cc_start: 0.8139 (ptt) cc_final: 0.7848 (pmm) REVERT: E 1088 ASP cc_start: 0.8333 (p0) cc_final: 0.8107 (m-30) REVERT: N 1 MET cc_start: 0.7659 (tmm) cc_final: 0.7261 (tmm) REVERT: N 49 PHE cc_start: 0.6927 (m-10) cc_final: 0.6707 (m-10) REVERT: N 106 ASP cc_start: 0.7778 (t0) cc_final: 0.7558 (m-30) REVERT: N 172 ILE cc_start: 0.6550 (mt) cc_final: 0.6260 (mt) REVERT: N 233 MET cc_start: 0.7365 (mmm) cc_final: 0.6754 (mmm) REVERT: N 294 PHE cc_start: 0.7623 (m-80) cc_final: 0.7306 (m-10) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1046 time to fit residues: 36.1512 Evaluate side-chains 178 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 30 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 141 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 chunk 5 optimal weight: 0.0980 chunk 109 optimal weight: 3.9990 chunk 124 optimal weight: 0.0050 chunk 125 optimal weight: 9.9990 chunk 110 optimal weight: 0.0970 overall best weight: 0.2070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1032 ASN ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 222 HIS ** N 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.115094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.095079 restraints weight = 53991.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.097988 restraints weight = 32190.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.100053 restraints weight = 21940.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.101467 restraints weight = 16409.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.102452 restraints weight = 13260.684| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16744 Z= 0.135 Angle : 0.707 8.496 23090 Z= 0.376 Chirality : 0.043 0.226 2612 Planarity : 0.005 0.052 2614 Dihedral : 20.780 176.855 3050 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.77 % Favored : 85.23 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.19), residues: 1788 helix: 0.84 (0.26), residues: 426 sheet: 0.04 (0.39), residues: 188 loop : -3.79 (0.15), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 909 TYR 0.021 0.002 TYR N 199 PHE 0.015 0.001 PHE E 640 TRP 0.020 0.002 TRP M 208 HIS 0.008 0.001 HIS N 161 Details of bonding type rmsd covalent geometry : bond 0.00295 (16734) covalent geometry : angle 0.70657 (23080) hydrogen bonds : bond 0.03748 ( 430) hydrogen bonds : angle 4.11968 ( 1140) metal coordination : bond 0.00460 ( 8) metal coordination : angle 1.43967 ( 4) link_TRANS : bond 0.00052 ( 2) link_TRANS : angle 0.20812 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2480.37 seconds wall clock time: 43 minutes 54.13 seconds (2634.13 seconds total)