Starting phenix.real_space_refine on Sat Sep 12 13:12:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6b40_7046/09_2026/6b40_7046.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b40_7046/09_2026/6b40_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6b40_7046/09_2026/6b40_7046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b40_7046/09_2026/6b40_7046.map" model { file = "/net/cci-nas-00/data/ceres_data/6b40_7046/09_2026/6b40_7046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b40_7046/09_2026/6b40_7046.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6b40_7046/09_2026/6b40_7046.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6b40_7046/09_2026/6b40_7046.cif" } 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-2.2.1-6174/lib/python3.11/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: 6.12, per 1000 atoms: 0.38 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: 1.66 Conformation dependent library (CDL) restraints added in 591.4 milliseconds 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: 1.77 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: 3.45 Time building geometry restraints manager: 2.09 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=" C1' DC B 51 " pdb=" N1 DC B 51 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.96e+01 bond pdb=" C1' DC F 51 " pdb=" N1 DC F 51 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" C3' DG H 4 " pdb=" C2' DG H 4 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.88e+01 bond pdb=" C3' DG D 4 " pdb=" C2' DG D 4 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.84e+01 bond pdb=" C1' DC B 53 " pdb=" N1 DC B 53 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.65e+01 ... (remaining 16729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 22587 3.29 - 6.57: 445 6.57 - 9.86: 42 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=" C3' DG D 5 " pdb=" C2' DG D 5 " pdb=" C1' DG D 5 " ideal model delta sigma weight residual 102.50 95.49 7.01 1.20e+00 6.94e-01 3.42e+01 angle pdb=" C3' DG H 5 " pdb=" C2' DG H 5 " pdb=" C1' DG H 5 " ideal model delta sigma weight residual 102.50 95.49 7.01 1.20e+00 6.94e-01 3.41e+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 ... (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 - 0.048: 1597 0.048 - 0.095: 711 0.095 - 0.143: 235 0.143 - 0.190: 53 0.190 - 0.238: 16 Chirality restraints: 2612 Sorted by residual: chirality pdb=" C1' DG H 5 " pdb=" O4' DG H 5 " pdb=" C2' DG H 5 " pdb=" N9 DG H 5 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C1' DG D 5 " pdb=" O4' DG D 5 " pdb=" C2' DG D 5 " pdb=" N9 DG D 5 " both_signs ideal model delta sigma weight residual False 2.43 2.20 0.24 2.00e-01 2.50e+01 1.38e+00 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 ... (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: 0.560 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.630 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 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= 0.504 Angle : 1.161 16.433 23090 Z= 0.721 Chirality : 0.061 0.238 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 are 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/Z covalent geometry : bond 0.00769 / 0.50 (16734) covalent geometry : angle 1.15477 / 0.72 (23080) hydrogen bonds : bond 0.19793 / 13.12 ( 430) hydrogen bonds : angle 7.84012 / 5.34 ( 1140) metal coordination : bond 0.12343 / 7.46 ( 8) metal coordination : angle 9.23063 / 4.70 ( 4) link_TRANS : bond 0.00312 / 0.16 ( 2) link_TRANS : angle 1.09506 / 0.59 ( 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 : 0.465 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: 0.8025 (mt-10) REVERT: A 1034 LEU cc_start: 0.8496 (mp) cc_final: 0.8263 (tt) REVERT: A 1038 ILE cc_start: 0.8978 (pt) cc_final: 0.8576 (pt) REVERT: M 197 TYR cc_start: 0.5294 (m-10) cc_final: 0.5030 (m-10) REVERT: M 234 VAL cc_start: 0.7755 (t) cc_final: 0.7479 (t) REVERT: E 759 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7938 (mt-10) REVERT: E 939 LYS cc_start: 0.8457 (tppt) cc_final: 0.8190 (tppt) REVERT: E 1003 MET cc_start: 0.6726 (mmm) cc_final: 0.4667 (mmm) REVERT: E 1034 LEU cc_start: 0.8471 (mp) cc_final: 0.8254 (tt) REVERT: E 1101 LEU cc_start: 0.9046 (mt) cc_final: 0.8833 (tt) REVERT: N 234 VAL cc_start: 0.7622 (t) cc_final: 0.7280 (t) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.1432 time to fit residues: 80.3844 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 : 0.536 ------------------------------------------------------------------------------- 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: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1032 ASN A1042 GLN ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 780 GLN E 792 HIS E1032 ASN E1042 GLN ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 47 GLN N 209 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.108098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.087802 restraints weight = 54186.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.090387 restraints weight = 33614.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.092207 restraints weight = 23620.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.093460 restraints weight = 18130.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.094343 restraints weight = 14982.146| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 16744 Z= 0.273 Angle : 0.958 11.878 23090 Z= 0.514 Chirality : 0.052 0.347 2612 Planarity : 0.007 0.070 2614 Dihedral : 21.953 179.742 3050 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 17.45 % Favored : 82.44 % Rotamer: Outliers : 0.13 % Allowed : 2.56 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.29 % 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 are not related in a simple way. whole: -4.63 (0.17), residues: 1788 helix: -1.23 (0.22), residues: 432 sheet: -2.14 (0.33), residues: 214 loop : -4.34 (0.14), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 314 TYR 0.021 0.002 TYR A 994 PHE 0.018 0.002 PHE A 873 TRP 0.019 0.003 TRP N 95 HIS 0.012 0.002 HIS N 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.27 (16734) covalent geometry : angle 0.95613 / 0.51 (23080) hydrogen bonds : bond 0.07115 / 4.80 ( 430) hydrogen bonds : angle 6.19264 / 4.23 ( 1140) metal coordination : bond 0.03795 / 2.35 ( 8) metal coordination : angle 4.34349 / 2.20 ( 4) link_TRANS : bond 0.00255 / 0.13 ( 2) link_TRANS : angle 0.29717 / 0.17 ( 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 278 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 0.493 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 595 MET cc_start: 0.7360 (mtt) cc_final: 0.7146 (mtt) REVERT: A 711 GLU cc_start: 0.7748 (pt0) cc_final: 0.7451 (tt0) REVERT: A 734 MET cc_start: 0.1877 (ptp) cc_final: 0.0705 (tpt) REVERT: A 759 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8170 (mt-10) REVERT: A 781 ARG cc_start: 0.8720 (ttt-90) cc_final: 0.8285 (ttt180) REVERT: A 995 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7533 (mmm-85) REVERT: M 197 TYR cc_start: 0.6796 (m-10) cc_final: 0.6478 (m-10) REVERT: M 234 VAL cc_start: 0.8844 (t) cc_final: 0.8354 (p) REVERT: M 274 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7374 (tm-30) REVERT: E 595 MET cc_start: 0.7227 (mtt) cc_final: 0.6943 (mtt) REVERT: E 665 LYS cc_start: 0.9029 (mptt) cc_final: 0.8725 (mmtt) REVERT: E 734 MET cc_start: 0.1964 (ptp) cc_final: 0.1015 (tpt) REVERT: E 759 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8213 (mt-10) REVERT: E 847 TYR cc_start: 0.7206 (m-80) cc_final: 0.6209 (m-80) REVERT: E 939 LYS cc_start: 0.9147 (tppt) cc_final: 0.8569 (tppt) REVERT: E 1034 LEU cc_start: 0.9064 (mp) cc_final: 0.8593 (tt) REVERT: N 234 VAL cc_start: 0.8901 (t) cc_final: 0.8495 (t) REVERT: N 273 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7458 (tpp) REVERT: N 319 MET cc_start: 0.7055 (mmt) cc_final: 0.6801 (mmp) outliers start: 2 outliers final: 0 residues processed: 276 average time/residue: 0.1355 time to fit residues: 54.3834 Evaluate side-chains 200 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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: 0.7980 chunk 85 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 151 optimal weight: 50.0000 chunk 107 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 GLN ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 GLN ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 GLN N 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.109391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089677 restraints weight = 55222.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.092458 restraints weight = 33777.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.094368 restraints weight = 23248.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.095708 restraints weight = 17631.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.096654 restraints weight = 14356.051| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16744 Z= 0.185 Angle : 0.839 10.194 23090 Z= 0.457 Chirality : 0.049 0.302 2612 Planarity : 0.006 0.058 2614 Dihedral : 21.672 177.975 3050 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 16.89 % Favored : 83.00 % Rotamer: Outliers : 0.06 % Allowed : 1.85 % Favored : 98.08 % 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 are not related in a simple way. whole: -4.32 (0.17), residues: 1788 helix: -0.78 (0.24), residues: 434 sheet: -2.02 (0.34), residues: 212 loop : -4.21 (0.15), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 36 TYR 0.028 0.002 TYR N 300 PHE 0.012 0.002 PHE A 640 TRP 0.018 0.002 TRP A 917 HIS 0.008 0.001 HIS M 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (16734) covalent geometry : angle 0.83890 / 0.46 (23080) hydrogen bonds : bond 0.06167 / 4.15 ( 430) hydrogen bonds : angle 5.52191 / 3.73 ( 1140) metal coordination : bond 0.01379 / 0.85 ( 8) metal coordination : angle 2.12847 / 1.08 ( 4) link_TRANS : bond 0.00094 / 0.05 ( 2) link_TRANS : angle 0.34118 / 0.20 ( 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 262 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.397 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: A 734 MET cc_start: 0.2071 (ptp) cc_final: 0.0972 (tpt) REVERT: A 759 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8271 (mt-10) REVERT: A 863 MET cc_start: 0.7842 (ptp) cc_final: 0.7617 (ptp) REVERT: A 931 GLU cc_start: 0.8846 (tt0) cc_final: 0.8260 (tp30) REVERT: A 1053 SER cc_start: 0.8506 (p) cc_final: 0.8254 (m) REVERT: M 1 MET cc_start: 0.7332 (tmm) cc_final: 0.7126 (tmm) REVERT: M 197 TYR cc_start: 0.6672 (m-10) cc_final: 0.6343 (m-10) REVERT: M 234 VAL cc_start: 0.8866 (t) cc_final: 0.8476 (t) REVERT: M 274 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7361 (tm-30) REVERT: M 352 MET cc_start: 0.6520 (ptp) cc_final: 0.6048 (ptp) REVERT: E 595 MET cc_start: 0.7163 (mtt) cc_final: 0.6927 (mtt) REVERT: E 734 MET cc_start: 0.2115 (ptp) cc_final: 0.1337 (tpt) REVERT: E 759 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8207 (mt-10) REVERT: E 856 ILE cc_start: 0.8793 (mm) cc_final: 0.8567 (mm) REVERT: E 927 ILE cc_start: 0.9464 (mm) cc_final: 0.9229 (tt) REVERT: E 939 LYS cc_start: 0.9067 (tppt) cc_final: 0.8474 (tppt) REVERT: E 1034 LEU cc_start: 0.9043 (mp) cc_final: 0.8544 (tt) REVERT: E 1053 SER cc_start: 0.8595 (p) cc_final: 0.8313 (m) REVERT: N 1 MET cc_start: 0.7279 (tmm) cc_final: 0.7069 (tmm) REVERT: N 197 TYR cc_start: 0.6702 (m-10) cc_final: 0.6474 (m-10) REVERT: N 234 VAL cc_start: 0.8916 (t) cc_final: 0.8467 (p) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.1253 time to fit residues: 48.1548 Evaluate side-chains 193 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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: 4.9990 chunk 80 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 136 optimal weight: 0.0980 chunk 172 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 HIS A 807 ASN A1042 GLN ** 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 ** E1093 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 = 0.3886 r_free = 0.3886 target = 0.110044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.090324 restraints weight = 54598.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093040 restraints weight = 33218.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.094941 restraints weight = 22981.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.096282 restraints weight = 17479.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097112 restraints weight = 14249.861| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3341 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= 0.166 Angle : 0.800 11.772 23090 Z= 0.435 Chirality : 0.048 0.294 2612 Planarity : 0.006 0.082 2614 Dihedral : 21.550 178.277 3050 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 16.89 % Favored : 83.00 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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 are not related in a simple way. whole: -4.16 (0.18), residues: 1788 helix: -0.46 (0.24), residues: 434 sheet: -1.98 (0.33), residues: 212 loop : -4.18 (0.15), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 752 TYR 0.024 0.002 TYR M 199 PHE 0.012 0.001 PHE A 640 TRP 0.057 0.003 TRP E 917 HIS 0.006 0.001 HIS M 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (16734) covalent geometry : angle 0.79992 / 0.44 (23080) hydrogen bonds : bond 0.05648 / 3.79 ( 430) hydrogen bonds : angle 5.26688 / 3.54 ( 1140) metal coordination : bond 0.01296 / 0.80 ( 8) metal coordination : angle 1.56195 / 0.78 ( 4) link_TRANS : bond 0.00059 / 0.03 ( 2) link_TRANS : angle 0.23334 / 0.13 ( 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 239 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.475 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: A 734 MET cc_start: 0.2350 (ptp) cc_final: 0.1425 (tpt) REVERT: A 759 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8242 (mt-10) REVERT: A 782 LEU cc_start: 0.9294 (tp) cc_final: 0.9084 (mm) REVERT: A 863 MET cc_start: 0.8089 (ptp) cc_final: 0.7679 (ptt) REVERT: A 931 GLU cc_start: 0.8811 (tt0) cc_final: 0.8187 (tp30) REVERT: A 1053 SER cc_start: 0.8530 (p) cc_final: 0.8314 (m) REVERT: M 197 TYR cc_start: 0.6680 (m-10) cc_final: 0.6440 (m-10) REVERT: M 226 TRP cc_start: 0.7848 (t60) cc_final: 0.7336 (t60) REVERT: M 352 MET cc_start: 0.6443 (ptp) cc_final: 0.5982 (ptp) REVERT: E 734 MET cc_start: 0.1921 (ptp) cc_final: 0.1143 (tpt) REVERT: E 759 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8339 (mt-10) REVERT: E 816 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8133 (mtp85) REVERT: E 927 ILE cc_start: 0.9437 (mm) cc_final: 0.9226 (tt) REVERT: E 939 LYS cc_start: 0.9095 (tppt) cc_final: 0.8476 (tppt) REVERT: E 1034 LEU cc_start: 0.9051 (mp) cc_final: 0.8564 (tt) REVERT: E 1053 SER cc_start: 0.8534 (p) cc_final: 0.8246 (m) REVERT: N 1 MET cc_start: 0.7316 (tmm) cc_final: 0.7051 (tmm) REVERT: N 197 TYR cc_start: 0.6669 (m-10) cc_final: 0.6388 (m-10) REVERT: N 234 VAL cc_start: 0.8592 (t) cc_final: 0.8342 (t) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1213 time to fit residues: 43.5607 Evaluate side-chains 191 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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: 8.9990 chunk 75 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 145 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS A1032 ASN ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** 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 = 0.3836 r_free = 0.3836 target = 0.106685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.087122 restraints weight = 55567.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089761 restraints weight = 34131.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.091612 restraints weight = 23782.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.092862 restraints weight = 18163.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.093763 restraints weight = 14932.915| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16744 Z= 0.243 Angle : 0.866 11.520 23090 Z= 0.465 Chirality : 0.050 0.327 2612 Planarity : 0.006 0.064 2614 Dihedral : 21.566 179.422 3050 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 18.51 % Favored : 81.43 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.29 % 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 are not related in a simple way. whole: -4.14 (0.18), residues: 1788 helix: -0.46 (0.24), residues: 438 sheet: -1.82 (0.35), residues: 198 loop : -4.18 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 207 TYR 0.027 0.002 TYR A 847 PHE 0.018 0.002 PHE E 640 TRP 0.045 0.003 TRP E 917 HIS 0.014 0.002 HIS M 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.24 (16734) covalent geometry : angle 0.86535 / 0.46 (23080) hydrogen bonds : bond 0.06084 / 4.05 ( 430) hydrogen bonds : angle 5.44631 / 3.68 ( 1140) metal coordination : bond 0.03223 / 2.00 ( 8) metal coordination : angle 2.51399 / 1.30 ( 4) link_TRANS : bond 0.00157 / 0.08 ( 2) link_TRANS : angle 0.19121 / 0.11 ( 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 229 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.598 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: A 668 GLU cc_start: 0.8751 (tt0) cc_final: 0.8228 (tm-30) REVERT: A 734 MET cc_start: 0.2209 (ptp) cc_final: 0.1077 (tpt) REVERT: A 759 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 809 MET cc_start: 0.7516 (mpp) cc_final: 0.7202 (mpp) REVERT: A 816 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8313 (mtp85) REVERT: A 863 MET cc_start: 0.7969 (ptp) cc_final: 0.7654 (ptp) REVERT: A 931 GLU cc_start: 0.8839 (tt0) cc_final: 0.8237 (tp30) REVERT: A 1053 SER cc_start: 0.8713 (p) cc_final: 0.8419 (m) REVERT: M 1 MET cc_start: 0.7407 (tmm) cc_final: 0.7184 (tmm) REVERT: M 226 TRP cc_start: 0.7961 (t60) cc_final: 0.7414 (t60) REVERT: M 352 MET cc_start: 0.6563 (ptp) cc_final: 0.6237 (ptp) REVERT: E 734 MET cc_start: 0.2099 (ptp) cc_final: 0.1272 (tpt) REVERT: E 759 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8269 (mt-10) REVERT: E 816 ARG cc_start: 0.8609 (mtp85) cc_final: 0.8372 (mtp85) REVERT: E 927 ILE cc_start: 0.9443 (mm) cc_final: 0.9227 (tt) REVERT: E 939 LYS cc_start: 0.9160 (tppt) cc_final: 0.8546 (tppt) REVERT: E 1038 ILE cc_start: 0.9258 (pt) cc_final: 0.8976 (mp) REVERT: E 1053 SER cc_start: 0.8650 (p) cc_final: 0.8365 (m) REVERT: N 1 MET cc_start: 0.7243 (tmm) cc_final: 0.6974 (tmm) REVERT: N 84 MET cc_start: 0.4520 (mtt) cc_final: 0.4317 (mtt) REVERT: N 233 MET cc_start: 0.8433 (mmm) cc_final: 0.8163 (mmm) REVERT: N 234 VAL cc_start: 0.8556 (t) cc_final: 0.8305 (t) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1277 time to fit residues: 43.5875 Evaluate side-chains 172 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 9.9990 chunk 167 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 91 optimal weight: 20.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** 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 = 0.3842 r_free = 0.3842 target = 0.107485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088090 restraints weight = 55675.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.090700 restraints weight = 34155.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.092498 restraints weight = 23833.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.093750 restraints weight = 18254.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.094527 restraints weight = 15048.206| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16744 Z= 0.204 Angle : 0.822 10.712 23090 Z= 0.445 Chirality : 0.048 0.327 2612 Planarity : 0.006 0.060 2614 Dihedral : 21.516 178.427 3050 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.34 % Favored : 82.66 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -4.08 (0.18), residues: 1788 helix: -0.38 (0.24), residues: 438 sheet: -1.93 (0.34), residues: 206 loop : -4.13 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 909 TYR 0.023 0.002 TYR A 847 PHE 0.009 0.002 PHE E 873 TRP 0.062 0.003 TRP A 917 HIS 0.008 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (16734) covalent geometry : angle 0.82143 / 0.45 (23080) hydrogen bonds : bond 0.05688 / 3.79 ( 430) hydrogen bonds : angle 5.25680 / 3.55 ( 1140) metal coordination : bond 0.02418 / 1.57 ( 8) metal coordination : angle 2.52665 / 1.21 ( 4) link_TRANS : bond 0.00118 / 0.06 ( 2) link_TRANS : angle 0.25947 / 0.15 ( 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 229 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.627 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: A 668 GLU cc_start: 0.8693 (tt0) cc_final: 0.8098 (tm-30) REVERT: A 734 MET cc_start: 0.1957 (ptp) cc_final: 0.0950 (tpt) REVERT: A 759 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8180 (mt-10) REVERT: A 816 ARG cc_start: 0.8605 (mtp85) cc_final: 0.8315 (mtp85) REVERT: A 863 MET cc_start: 0.8232 (ptp) cc_final: 0.7865 (ptt) REVERT: A 931 GLU cc_start: 0.8833 (tt0) cc_final: 0.8239 (tp30) REVERT: A 1053 SER cc_start: 0.8633 (p) cc_final: 0.8383 (m) REVERT: M 1 MET cc_start: 0.7384 (tmm) cc_final: 0.7152 (tmm) REVERT: M 244 HIS cc_start: 0.6484 (m-70) cc_final: 0.6258 (m90) REVERT: M 352 MET cc_start: 0.6842 (ptp) cc_final: 0.6584 (ptp) REVERT: E 668 GLU cc_start: 0.8649 (tt0) cc_final: 0.8302 (tm-30) REVERT: E 734 MET cc_start: 0.2276 (ptp) cc_final: 0.1366 (tpt) REVERT: E 759 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8211 (mt-10) REVERT: E 816 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8253 (mtp85) REVERT: E 927 ILE cc_start: 0.9433 (mm) cc_final: 0.9220 (tt) REVERT: E 939 LYS cc_start: 0.9138 (tppt) cc_final: 0.8489 (tppt) REVERT: E 1038 ILE cc_start: 0.9254 (pt) cc_final: 0.8953 (mp) REVERT: E 1053 SER cc_start: 0.8636 (p) cc_final: 0.8368 (m) REVERT: N 1 MET cc_start: 0.7244 (tmm) cc_final: 0.6978 (tmm) REVERT: N 84 MET cc_start: 0.4642 (mtt) cc_final: 0.4415 (mtt) REVERT: N 234 VAL cc_start: 0.8585 (t) cc_final: 0.8335 (t) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1260 time to fit residues: 43.2463 Evaluate side-chains 173 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 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: 7.9990 chunk 118 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.107339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.087414 restraints weight = 55321.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.090149 restraints weight = 33756.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.091980 restraints weight = 23371.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093252 restraints weight = 17936.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.094142 restraints weight = 14759.366| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4086 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= 0.193 Angle : 0.817 12.161 23090 Z= 0.439 Chirality : 0.049 0.331 2612 Planarity : 0.006 0.072 2614 Dihedral : 21.523 178.263 3050 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.06 % Favored : 81.94 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -3.98 (0.18), residues: 1788 helix: -0.20 (0.24), residues: 436 sheet: -1.87 (0.35), residues: 204 loop : -4.10 (0.15), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 909 TYR 0.024 0.002 TYR A 847 PHE 0.013 0.002 PHE E 657 TRP 0.052 0.003 TRP A 917 HIS 0.006 0.001 HIS M 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (16734) covalent geometry : angle 0.81682 / 0.44 (23080) hydrogen bonds : bond 0.05511 / 3.63 ( 430) hydrogen bonds : angle 5.15476 / 3.49 ( 1140) metal coordination : bond 0.01887 / 1.18 ( 8) metal coordination : angle 2.67194 / 1.35 ( 4) link_TRANS : bond 0.00108 / 0.05 ( 2) link_TRANS : angle 0.25795 / 0.15 ( 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 232 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.596 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: A 668 GLU cc_start: 0.8691 (tt0) cc_final: 0.8207 (tm-30) REVERT: A 703 MET cc_start: 0.8983 (tpp) cc_final: 0.8414 (mmm) REVERT: A 734 MET cc_start: 0.1807 (ptp) cc_final: 0.0783 (tpt) REVERT: A 759 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8164 (mt-10) REVERT: A 809 MET cc_start: 0.7571 (mpp) cc_final: 0.7163 (mpp) REVERT: A 816 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8391 (mtp85) REVERT: A 863 MET cc_start: 0.8224 (ptp) cc_final: 0.7902 (ptt) REVERT: A 931 GLU cc_start: 0.8869 (tt0) cc_final: 0.8289 (tp30) REVERT: A 1053 SER cc_start: 0.8614 (p) cc_final: 0.8363 (m) REVERT: M 1 MET cc_start: 0.7421 (tmm) cc_final: 0.7190 (tmm) REVERT: M 234 VAL cc_start: 0.8513 (t) cc_final: 0.8267 (t) REVERT: E 668 GLU cc_start: 0.8843 (tt0) cc_final: 0.8290 (tm-30) REVERT: E 703 MET cc_start: 0.9057 (tpp) cc_final: 0.8506 (mmm) REVERT: E 734 MET cc_start: 0.2059 (ptp) cc_final: 0.1295 (tpt) REVERT: E 759 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8202 (mt-10) REVERT: E 760 CYS cc_start: 0.7840 (t) cc_final: 0.7615 (t) REVERT: E 847 TYR cc_start: 0.6669 (m-80) cc_final: 0.6426 (m-80) REVERT: E 927 ILE cc_start: 0.9386 (mm) cc_final: 0.9154 (tt) REVERT: E 939 LYS cc_start: 0.9155 (tppt) cc_final: 0.8516 (tppt) REVERT: E 1038 ILE cc_start: 0.9245 (pt) cc_final: 0.8929 (mp) REVERT: E 1053 SER cc_start: 0.8614 (p) cc_final: 0.8354 (m) REVERT: N 1 MET cc_start: 0.7255 (tmm) cc_final: 0.7025 (tmm) REVERT: N 84 MET cc_start: 0.4657 (mtt) cc_final: 0.4419 (mtt) REVERT: N 233 MET cc_start: 0.8142 (mmm) cc_final: 0.7510 (mmm) REVERT: N 234 VAL cc_start: 0.8543 (t) cc_final: 0.8334 (p) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1268 time to fit residues: 43.6577 Evaluate side-chains 175 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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: 9.9990 chunk 65 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.109190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.089532 restraints weight = 56028.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.092265 restraints weight = 34099.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094151 restraints weight = 23591.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.095470 restraints weight = 17919.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.096343 restraints weight = 14652.130| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 16744 Z= 0.164 Angle : 0.798 12.830 23090 Z= 0.430 Chirality : 0.047 0.328 2612 Planarity : 0.006 0.091 2614 Dihedral : 21.513 178.047 3050 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.39 % Favored : 83.61 % 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 : 0.24 % 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 are not related in a simple way. whole: -3.80 (0.18), residues: 1788 helix: -0.02 (0.24), residues: 446 sheet: -1.39 (0.37), residues: 194 loop : -4.09 (0.15), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 207 TYR 0.021 0.002 TYR A 847 PHE 0.013 0.001 PHE E 640 TRP 0.033 0.003 TRP A 917 HIS 0.007 0.001 HIS E 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (16734) covalent geometry : angle 0.79738 / 0.43 (23080) hydrogen bonds : bond 0.05212 / 3.40 ( 430) hydrogen bonds : angle 4.90269 / 3.31 ( 1140) metal coordination : bond 0.00993 / 0.63 ( 8) metal coordination : angle 2.18834 / 1.07 ( 4) link_TRANS : bond 0.00057 / 0.03 ( 2) link_TRANS : angle 0.29251 / 0.17 ( 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 236 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 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: A 547 MET cc_start: 0.7381 (tmm) cc_final: 0.6806 (tmm) REVERT: A 561 MET cc_start: 0.8002 (ttt) cc_final: 0.7705 (ttt) REVERT: A 668 GLU cc_start: 0.8678 (tt0) cc_final: 0.8217 (tm-30) REVERT: A 734 MET cc_start: 0.1949 (ptp) cc_final: 0.1142 (tpt) REVERT: A 759 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8141 (mt-10) REVERT: A 793 MET cc_start: 0.6329 (tmm) cc_final: 0.5729 (ptt) REVERT: A 816 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8400 (mtp85) REVERT: A 856 ILE cc_start: 0.8862 (mm) cc_final: 0.8654 (mm) REVERT: A 931 GLU cc_start: 0.8862 (tt0) cc_final: 0.8278 (tp30) REVERT: M 1 MET cc_start: 0.7411 (tmm) cc_final: 0.7183 (tmm) REVERT: M 259 LYS cc_start: 0.6166 (pttp) cc_final: 0.5857 (tppt) REVERT: E 668 GLU cc_start: 0.8785 (tt0) cc_final: 0.8298 (tm-30) REVERT: E 734 MET cc_start: 0.2370 (ptp) cc_final: 0.1747 (tpt) REVERT: E 759 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8213 (mt-10) REVERT: E 847 TYR cc_start: 0.6588 (m-80) cc_final: 0.6349 (m-80) REVERT: E 909 ARG cc_start: 0.8962 (mmt90) cc_final: 0.8725 (mtt180) REVERT: E 927 ILE cc_start: 0.9365 (mm) cc_final: 0.9124 (tt) REVERT: E 939 LYS cc_start: 0.9073 (tppt) cc_final: 0.8457 (tppt) REVERT: E 1038 ILE cc_start: 0.9254 (pt) cc_final: 0.8942 (mp) REVERT: E 1053 SER cc_start: 0.8449 (p) cc_final: 0.8227 (m) REVERT: N 1 MET cc_start: 0.7282 (tmm) cc_final: 0.7056 (tmm) REVERT: N 84 MET cc_start: 0.4710 (mtt) cc_final: 0.4508 (mtt) REVERT: N 233 MET cc_start: 0.8083 (mmm) cc_final: 0.7521 (mmm) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1251 time to fit residues: 43.6960 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 : 0.560 ------------------------------------------------------------------------------- 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: 2.9990 chunk 129 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 54 optimal weight: 30.0000 chunk 157 optimal weight: 0.1980 chunk 143 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1032 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.110322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.090768 restraints weight = 55188.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.093472 restraints weight = 33381.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.095359 restraints weight = 23138.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.096676 restraints weight = 17618.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.097480 restraints weight = 14417.939| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16744 Z= 0.154 Angle : 0.800 11.202 23090 Z= 0.429 Chirality : 0.048 0.326 2612 Planarity : 0.006 0.089 2614 Dihedral : 21.545 178.347 3050 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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 are not related in a simple way. whole: -3.68 (0.18), residues: 1788 helix: 0.10 (0.24), residues: 450 sheet: -1.18 (0.38), residues: 194 loop : -4.08 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 344 TYR 0.021 0.002 TYR E 828 PHE 0.013 0.001 PHE N 294 TRP 0.061 0.003 TRP A 917 HIS 0.009 0.001 HIS E 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (16734) covalent geometry : angle 0.79959 / 0.43 (23080) hydrogen bonds : bond 0.05052 / 3.28 ( 430) hydrogen bonds : angle 4.78605 / 3.25 ( 1140) metal coordination : bond 0.00663 / 0.43 ( 8) metal coordination : angle 1.93887 / 0.92 ( 4) link_TRANS : bond 0.00025 / 0.01 ( 2) link_TRANS : angle 0.28699 / 0.16 ( 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 235 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 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: A 547 MET cc_start: 0.7212 (tmm) cc_final: 0.6696 (tmm) REVERT: A 561 MET cc_start: 0.7939 (ttt) cc_final: 0.7614 (ttp) REVERT: A 668 GLU cc_start: 0.8831 (tt0) cc_final: 0.8336 (tm-30) REVERT: A 734 MET cc_start: 0.1873 (ptp) cc_final: 0.1147 (tpt) REVERT: A 759 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8106 (mt-10) REVERT: A 793 MET cc_start: 0.6514 (tmm) cc_final: 0.5689 (ptt) REVERT: A 816 ARG cc_start: 0.8653 (mtp85) cc_final: 0.8427 (mtp85) REVERT: A 931 GLU cc_start: 0.8829 (tt0) cc_final: 0.8247 (tp30) REVERT: M 1 MET cc_start: 0.7376 (tmm) cc_final: 0.7110 (tmm) REVERT: M 259 LYS cc_start: 0.6221 (pttp) cc_final: 0.5719 (tppt) REVERT: M 273 MET cc_start: 0.7947 (tpp) cc_final: 0.7687 (tpp) REVERT: E 734 MET cc_start: 0.2224 (ptp) cc_final: 0.1696 (tpt) REVERT: E 759 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8157 (mt-10) REVERT: E 857 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7710 (tm-30) REVERT: E 931 GLU cc_start: 0.8866 (tt0) cc_final: 0.8155 (tp30) REVERT: E 939 LYS cc_start: 0.9029 (tppt) cc_final: 0.8399 (tppt) REVERT: E 1038 ILE cc_start: 0.9326 (pt) cc_final: 0.9057 (mp) REVERT: N 1 MET cc_start: 0.7256 (tmm) cc_final: 0.7029 (tmm) REVERT: N 84 MET cc_start: 0.4737 (mtt) cc_final: 0.4524 (mtt) REVERT: N 233 MET cc_start: 0.7986 (mmm) cc_final: 0.7434 (mmm) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1217 time to fit residues: 43.0373 Evaluate side-chains 169 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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: 5.9990 chunk 58 optimal weight: 0.0670 chunk 43 optimal weight: 10.0000 chunk 149 optimal weight: 30.0000 chunk 131 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 126 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.111956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.092152 restraints weight = 54655.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095029 restraints weight = 32946.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.096986 restraints weight = 22564.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.098332 restraints weight = 17017.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.099271 restraints weight = 13837.547| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16744 Z= 0.142 Angle : 0.769 11.057 23090 Z= 0.414 Chirality : 0.047 0.326 2612 Planarity : 0.005 0.074 2614 Dihedral : 21.456 178.658 3050 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.49 % Favored : 84.51 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -3.54 (0.18), residues: 1788 helix: 0.18 (0.24), residues: 450 sheet: -0.98 (0.36), residues: 214 loop : -4.03 (0.15), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 909 TYR 0.020 0.002 TYR N 197 PHE 0.014 0.001 PHE E 640 TRP 0.075 0.003 TRP A 917 HIS 0.009 0.001 HIS A 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (16734) covalent geometry : angle 0.76885 / 0.41 (23080) hydrogen bonds : bond 0.04708 / 3.07 ( 430) hydrogen bonds : angle 4.61283 / 3.13 ( 1140) metal coordination : bond 0.00301 / 0.18 ( 8) metal coordination : angle 1.89655 / 0.90 ( 4) link_TRANS : bond 0.00014 / 0.01 ( 2) link_TRANS : angle 0.29466 / 0.17 ( 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 246 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.560 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 561 MET cc_start: 0.7826 (ttt) cc_final: 0.7553 (ttp) REVERT: A 668 GLU cc_start: 0.8736 (tt0) cc_final: 0.8344 (tm-30) REVERT: A 734 MET cc_start: 0.2094 (ptp) cc_final: 0.1732 (tpt) REVERT: A 759 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8100 (mt-10) REVERT: A 793 MET cc_start: 0.6497 (tmm) cc_final: 0.5623 (ptt) REVERT: A 809 MET cc_start: 0.7587 (mpp) cc_final: 0.6995 (mpp) REVERT: A 816 ARG cc_start: 0.8649 (mtp85) cc_final: 0.8394 (mtp85) REVERT: A 909 ARG cc_start: 0.8752 (mmt90) cc_final: 0.8264 (mmt180) REVERT: A 931 GLU cc_start: 0.8839 (tt0) cc_final: 0.8245 (tp30) REVERT: M 273 MET cc_start: 0.7773 (tpp) cc_final: 0.7258 (tpp) REVERT: E 561 MET cc_start: 0.7835 (ttt) cc_final: 0.7621 (ttp) REVERT: E 669 GLU cc_start: 0.8312 (tp30) cc_final: 0.8069 (tp30) REVERT: E 734 MET cc_start: 0.2088 (ptp) cc_final: 0.1682 (tpt) REVERT: E 759 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8113 (mt-10) REVERT: E 847 TYR cc_start: 0.6384 (m-80) cc_final: 0.6040 (m-80) REVERT: E 857 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7743 (tm-30) REVERT: E 931 GLU cc_start: 0.8843 (tt0) cc_final: 0.8156 (tp30) REVERT: E 939 LYS cc_start: 0.9018 (tppt) cc_final: 0.8324 (tppt) REVERT: E 1038 ILE cc_start: 0.9306 (pt) cc_final: 0.9024 (mp) REVERT: N 1 MET cc_start: 0.7156 (tmm) cc_final: 0.6941 (tmm) REVERT: N 84 MET cc_start: 0.4581 (mtt) cc_final: 0.4369 (mtt) REVERT: N 233 MET cc_start: 0.8011 (mmm) cc_final: 0.7493 (mmm) REVERT: N 302 HIS cc_start: 0.6344 (t-90) cc_final: 0.6058 (t70) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1250 time to fit residues: 46.0581 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 : 0.551 ------------------------------------------------------------------------------- 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: 4.9990 chunk 144 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 141 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 124 optimal weight: 0.2980 chunk 125 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.110140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.090724 restraints weight = 55192.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093485 restraints weight = 33450.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095337 restraints weight = 23027.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.096598 restraints weight = 17558.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.097489 restraints weight = 14407.782| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16744 Z= 0.169 Angle : 0.784 10.588 23090 Z= 0.421 Chirality : 0.047 0.339 2612 Planarity : 0.006 0.086 2614 Dihedral : 21.430 178.827 3050 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.61 % Favored : 83.39 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -3.49 (0.19), residues: 1788 helix: 0.24 (0.24), residues: 450 sheet: -0.78 (0.38), residues: 194 loop : -4.00 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 909 TYR 0.019 0.002 TYR A 847 PHE 0.011 0.001 PHE E 640 TRP 0.048 0.002 TRP A 917 HIS 0.007 0.001 HIS E 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (16734) covalent geometry : angle 0.78335 / 0.42 (23080) hydrogen bonds : bond 0.04920 / 3.22 ( 430) hydrogen bonds : angle 4.72707 / 3.22 ( 1140) metal coordination : bond 0.01422 / 0.89 ( 8) metal coordination : angle 2.05816 / 0.96 ( 4) link_TRANS : bond 0.00069 / 0.03 ( 2) link_TRANS : angle 0.28366 / 0.16 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2379.84 seconds wall clock time: 42 minutes 55.25 seconds (2575.25 seconds total)