Starting phenix.real_space_refine on Sun Mar 17 00:28:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b40_7046/03_2024/6b40_7046.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b40_7046/03_2024/6b40_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b40_7046/03_2024/6b40_7046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b40_7046/03_2024/6b40_7046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b40_7046/03_2024/6b40_7046.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b40_7046/03_2024/6b40_7046.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 837": "NH1" <-> "NH2" Residue "E PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 837": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16202 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4315 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 528} Chain breaks: 1 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: "E" Number of atoms: 4315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4315 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 528} Chain breaks: 1 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: "F" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "G" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "H" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "N" 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} Chain: "E" 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 ATOM 10119 SG CYS E 830 57.939 25.350 61.148 1.00 50.00 S ATOM 10140 SG CYS E 833 56.760 22.413 63.940 1.00 50.00 S Time building chain proxies: 9.23, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.15 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 6.02 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: 6.98 Time building geometry restraints manager: 7.66 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: 3767 1.33 - 1.45: 3795 1.45 - 1.57: 8808 1.57 - 1.69: 194 1.69 - 1.81: 172 Bond restraints: 16736 Sorted by residual: bond pdb=" C TYR E 878 " pdb=" N PRO E 879 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.19e+00 bond pdb=" C TYR A 878 " pdb=" N PRO A 879 " ideal model delta sigma weight residual 1.334 1.381 -0.048 2.34e-02 1.83e+03 4.13e+00 bond pdb=" CB ILE M 172 " pdb=" CG2 ILE M 172 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" CB ILE N 172 " pdb=" CG2 ILE N 172 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" C ASP E 684 " pdb=" N PRO E 685 " ideal model delta sigma weight residual 1.340 1.394 -0.054 2.76e-02 1.31e+03 3.83e+00 ... (remaining 16731 not shown) Histogram of bond angle deviations from ideal: 95.49 - 104.59: 701 104.59 - 113.69: 9904 113.69 - 122.79: 10318 122.79 - 131.89: 2111 131.89 - 140.99: 52 Bond angle restraints: 23086 Sorted by residual: angle pdb=" C ASN A 747 " pdb=" N PRO A 748 " pdb=" CD PRO A 748 " ideal model delta sigma weight residual 120.60 104.17 16.43 2.20e+00 2.07e-01 5.58e+01 angle pdb=" C ASN E 747 " pdb=" N PRO E 748 " pdb=" CD PRO E 748 " ideal model delta sigma weight residual 120.60 104.18 16.42 2.20e+00 2.07e-01 5.57e+01 angle pdb=" C ASN E 747 " pdb=" N PRO E 748 " pdb=" CA PRO E 748 " ideal model delta sigma weight residual 127.00 140.99 -13.99 2.40e+00 1.74e-01 3.40e+01 angle pdb=" C ASN A 747 " pdb=" N PRO A 748 " pdb=" CA PRO A 748 " ideal model delta sigma weight residual 127.00 140.97 -13.97 2.40e+00 1.74e-01 3.39e+01 angle pdb=" N LEU N 173 " pdb=" CA LEU N 173 " pdb=" C LEU N 173 " ideal model delta sigma weight residual 109.24 116.68 -7.44 1.67e+00 3.59e-01 1.98e+01 ... (remaining 23081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 9430 34.43 - 68.86: 446 68.86 - 103.29: 12 103.29 - 137.72: 0 137.72 - 172.15: 4 Dihedral angle restraints: 9892 sinusoidal: 4568 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 9889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1586 0.046 - 0.091: 729 0.091 - 0.137: 225 0.137 - 0.182: 54 0.182 - 0.228: 18 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CB ILE E 695 " pdb=" CA ILE E 695 " pdb=" CG1 ILE E 695 " pdb=" CG2 ILE E 695 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE N 172 " pdb=" N ILE N 172 " pdb=" C ILE N 172 " pdb=" CB ILE N 172 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE A 695 " pdb=" CA ILE A 695 " pdb=" CG1 ILE A 695 " pdb=" CG2 ILE A 695 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2609 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 747 " -0.048 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO A 748 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 748 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 748 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 747 " -0.048 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO E 748 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 748 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 748 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 135 " 0.047 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO N 136 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO N 136 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 136 " 0.039 5.00e-02 4.00e+02 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3920 2.79 - 3.32: 14738 3.32 - 3.85: 27250 3.85 - 4.37: 29910 4.37 - 4.90: 47521 Nonbonded interactions: 123339 Sorted by model distance: nonbonded pdb=" NZ LYS A 563 " pdb=" OP2 DA G 8 " model vdw 2.269 2.520 nonbonded pdb=" OD2 ASP A 891 " pdb=" OG SER A1059 " model vdw 2.279 2.440 nonbonded pdb=" OD2 ASP E 891 " pdb=" OG SER E1059 " model vdw 2.279 2.440 nonbonded pdb=" OG SER M 284 " pdb=" O GLY M 298 " model vdw 2.281 2.440 nonbonded pdb=" OG SER N 284 " pdb=" O GLY N 298 " model vdw 2.281 2.440 ... (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 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: 0.570 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: 0.030 Extract box with map and model: 2.370 Check model and map are aligned: 0.250 Set scattering table: 0.180 Process input model: 52.840 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 16736 Z= 0.465 Angle : 1.128 16.433 23086 Z= 0.622 Chirality : 0.059 0.228 2612 Planarity : 0.008 0.090 2616 Dihedral : 16.849 172.154 6456 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.035 0.004 TRP A 917 HIS 0.012 0.003 HIS A 693 PHE 0.024 0.004 PHE A 873 TYR 0.032 0.003 TYR A 994 ARG 0.012 0.001 ARG M 334 *********************** 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 fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 1.980 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: 0.8022 (mt-10) REVERT: A 1034 LEU cc_start: 0.8496 (mp) cc_final: 0.8262 (tt) REVERT: A 1038 ILE cc_start: 0.8978 (pt) cc_final: 0.8581 (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: 0.7476 (t) REVERT: E 759 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7954 (mt-10) REVERT: E 939 LYS cc_start: 0.8457 (tppt) cc_final: 0.8197 (tppt) REVERT: E 1003 MET cc_start: 0.6726 (mmm) cc_final: 0.4634 (mmm) REVERT: E 1034 LEU cc_start: 0.8471 (mp) cc_final: 0.8251 (tt) REVERT: E 1101 LEU cc_start: 0.9046 (mt) cc_final: 0.8832 (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: 0.3409 time to fit residues: 187.7673 Evaluate side-chains 211 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 172 optimal weight: 20.0000 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 HIS A1032 ASN A1042 GLN ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 GLN M 361 ASN ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 792 HIS E1032 ASN E1042 GLN ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 47 GLN N 129 GLN N 209 ASN N 361 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16736 Z= 0.250 Angle : 0.791 9.354 23086 Z= 0.424 Chirality : 0.045 0.174 2612 Planarity : 0.006 0.064 2616 Dihedral : 21.559 175.078 3052 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 15.72 % Favored : 84.06 % Rotamer: Outliers : 0.19 % Allowed : 2.37 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.17), residues: 1788 helix: -0.96 (0.23), residues: 436 sheet: -2.07 (0.35), residues: 190 loop : -4.23 (0.14), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 917 HIS 0.006 0.001 HIS E 693 PHE 0.013 0.002 PHE A 640 TYR 0.024 0.002 TYR A 828 ARG 0.007 0.001 ARG M 207 *********************** 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 305 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 302 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 MET cc_start: 0.1512 (ptp) cc_final: 0.1128 (tpt) REVERT: A 816 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7898 (mtt-85) REVERT: A 847 TYR cc_start: 0.6712 (m-80) cc_final: 0.6002 (m-80) REVERT: A 995 ARG cc_start: 0.7223 (mmm-85) cc_final: 0.6720 (mmm-85) REVERT: A 1034 LEU cc_start: 0.8676 (mp) cc_final: 0.8215 (tt) REVERT: M 234 VAL cc_start: 0.7528 (t) cc_final: 0.7323 (t) REVERT: E 638 MET cc_start: 0.7696 (mtm) cc_final: 0.7446 (mtp) REVERT: E 711 GLU cc_start: 0.7697 (pt0) cc_final: 0.7331 (tt0) REVERT: E 847 TYR cc_start: 0.6685 (m-80) cc_final: 0.6027 (m-80) REVERT: E 858 VAL cc_start: 0.8300 (m) cc_final: 0.8093 (m) REVERT: E 939 LYS cc_start: 0.8584 (tppt) cc_final: 0.8204 (tppt) outliers start: 3 outliers final: 0 residues processed: 304 average time/residue: 0.3036 time to fit residues: 132.9916 Evaluate side-chains 186 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 143 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 186 optimal weight: 0.0050 chunk 153 optimal weight: 10.0000 chunk 171 optimal weight: 0.3980 chunk 58 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 780 GLN ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 ASN ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 780 GLN N 329 HIS N 361 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16736 Z= 0.221 Angle : 0.745 8.051 23086 Z= 0.401 Chirality : 0.044 0.179 2612 Planarity : 0.005 0.056 2616 Dihedral : 21.240 175.464 3052 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.44 % Favored : 83.50 % Rotamer: Outliers : 0.06 % Allowed : 2.17 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.18), residues: 1788 helix: -0.14 (0.24), residues: 432 sheet: -1.82 (0.33), residues: 214 loop : -4.16 (0.15), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 917 HIS 0.007 0.001 HIS M 161 PHE 0.012 0.001 PHE A 640 TYR 0.021 0.001 TYR A 828 ARG 0.007 0.001 ARG E 909 *********************** 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 256 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 GLU cc_start: 0.7701 (pt0) cc_final: 0.7056 (tt0) REVERT: A 734 MET cc_start: 0.1345 (ptp) cc_final: 0.1003 (tpt) REVERT: A 816 ARG cc_start: 0.8326 (mtp85) cc_final: 0.8056 (mtt-85) REVERT: M 84 MET cc_start: 0.3532 (mtt) cc_final: 0.3177 (mtt) REVERT: E 638 MET cc_start: 0.7688 (mtm) cc_final: 0.7383 (mtp) REVERT: E 711 GLU cc_start: 0.7822 (pt0) cc_final: 0.7403 (tt0) REVERT: E 856 ILE cc_start: 0.8229 (mm) cc_final: 0.7846 (mm) REVERT: E 939 LYS cc_start: 0.8456 (tppt) cc_final: 0.8028 (tppt) REVERT: N 84 MET cc_start: 0.3585 (mtt) cc_final: 0.3215 (mtt) outliers start: 1 outliers final: 1 residues processed: 256 average time/residue: 0.3138 time to fit residues: 118.3691 Evaluate side-chains 176 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 5.9990 chunk 129 optimal weight: 0.0050 chunk 89 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 116 optimal weight: 0.0060 chunk 173 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 0.9412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 ASN ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16736 Z= 0.192 Angle : 0.704 8.252 23086 Z= 0.379 Chirality : 0.043 0.226 2612 Planarity : 0.005 0.056 2616 Dihedral : 21.115 175.939 3052 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.11 % Favored : 83.89 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.18), residues: 1788 helix: 0.29 (0.25), residues: 436 sheet: -1.46 (0.34), residues: 206 loop : -4.07 (0.15), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 917 HIS 0.006 0.001 HIS A 693 PHE 0.011 0.001 PHE A 640 TYR 0.018 0.001 TYR A 828 ARG 0.007 0.000 ARG A 909 *********************** 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 260 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.839 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: A 668 GLU cc_start: 0.7879 (tt0) cc_final: 0.7503 (tm-30) REVERT: A 711 GLU cc_start: 0.7629 (pt0) cc_final: 0.7406 (tt0) REVERT: A 995 ARG cc_start: 0.7319 (mmm-85) cc_final: 0.6877 (mmm-85) REVERT: M 84 MET cc_start: 0.3522 (mtt) cc_final: 0.3083 (mtt) REVERT: E 638 MET cc_start: 0.7605 (mtm) cc_final: 0.7319 (mtp) REVERT: E 668 GLU cc_start: 0.7918 (tt0) cc_final: 0.7706 (tm-30) REVERT: E 703 MET cc_start: 0.8704 (tpp) cc_final: 0.8502 (tpp) REVERT: E 858 VAL cc_start: 0.8277 (m) cc_final: 0.7690 (m) REVERT: E 939 LYS cc_start: 0.8371 (tppt) cc_final: 0.7947 (tptt) REVERT: E 1038 ILE cc_start: 0.8838 (pt) cc_final: 0.8544 (mt) REVERT: N 84 MET cc_start: 0.3618 (mtt) cc_final: 0.3334 (mtt) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2904 time to fit residues: 111.8406 Evaluate side-chains 170 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 164 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 ASN E1024 HIS ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 361 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16736 Z= 0.234 Angle : 0.733 8.895 23086 Z= 0.394 Chirality : 0.043 0.197 2612 Planarity : 0.005 0.060 2616 Dihedral : 21.206 176.869 3052 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.72 % Favored : 83.28 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.18), residues: 1788 helix: 0.47 (0.25), residues: 432 sheet: -1.27 (0.34), residues: 210 loop : -4.02 (0.15), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 917 HIS 0.005 0.001 HIS M 161 PHE 0.011 0.001 PHE A 657 TYR 0.019 0.002 TYR A 828 ARG 0.009 0.001 ARG A 909 *********************** 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 237 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 668 GLU cc_start: 0.7808 (tt0) cc_final: 0.7546 (tm-30) REVERT: E 638 MET cc_start: 0.7511 (mtm) cc_final: 0.7283 (mtp) REVERT: E 858 VAL cc_start: 0.8310 (m) cc_final: 0.7931 (m) REVERT: E 939 LYS cc_start: 0.8334 (tppt) cc_final: 0.7925 (tppt) REVERT: N 233 MET cc_start: 0.5052 (mmm) cc_final: 0.4693 (mmm) REVERT: N 234 VAL cc_start: 0.7137 (t) cc_final: 0.6919 (p) REVERT: N 273 MET cc_start: 0.4979 (tpp) cc_final: 0.4632 (tpp) REVERT: N 294 PHE cc_start: 0.6313 (m-10) cc_final: 0.5970 (m-10) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2778 time to fit residues: 98.5475 Evaluate side-chains 168 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 30.0000 chunk 96 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 ASN ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16736 Z= 0.219 Angle : 0.722 9.075 23086 Z= 0.387 Chirality : 0.043 0.194 2612 Planarity : 0.005 0.051 2616 Dihedral : 21.066 176.181 3052 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.88 % Favored : 84.12 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.19), residues: 1788 helix: 0.70 (0.25), residues: 432 sheet: -1.13 (0.34), residues: 210 loop : -3.96 (0.15), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 917 HIS 0.006 0.001 HIS A 693 PHE 0.010 0.001 PHE A 640 TYR 0.019 0.001 TYR M 199 ARG 0.004 0.000 ARG E 956 *********************** 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 226 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.797 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 761 ILE cc_start: 0.8870 (mt) cc_final: 0.8326 (mt) REVERT: A 809 MET cc_start: 0.7605 (mpp) cc_final: 0.7190 (mpp) REVERT: M 84 MET cc_start: 0.4309 (mtt) cc_final: 0.3854 (mtt) REVERT: M 294 PHE cc_start: 0.5615 (m-80) cc_final: 0.5383 (m-10) REVERT: E 547 MET cc_start: 0.7227 (tmm) cc_final: 0.7000 (tmm) REVERT: E 939 LYS cc_start: 0.8354 (tppt) cc_final: 0.7896 (tppt) REVERT: E 995 ARG cc_start: 0.7475 (mmm160) cc_final: 0.6669 (mmm-85) REVERT: N 84 MET cc_start: 0.4407 (mtt) cc_final: 0.3978 (mtt) REVERT: N 234 VAL cc_start: 0.7311 (t) cc_final: 0.7080 (p) REVERT: N 273 MET cc_start: 0.5299 (tpp) cc_final: 0.4868 (tpp) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2785 time to fit residues: 94.2536 Evaluate side-chains 169 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 340 HIS M 361 ASN ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 361 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16736 Z= 0.207 Angle : 0.706 8.896 23086 Z= 0.379 Chirality : 0.043 0.185 2612 Planarity : 0.005 0.081 2616 Dihedral : 20.970 176.343 3052 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.28 % Favored : 83.72 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.19), residues: 1788 helix: 0.86 (0.25), residues: 432 sheet: -0.93 (0.34), residues: 208 loop : -3.93 (0.15), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 917 HIS 0.006 0.001 HIS A 693 PHE 0.013 0.001 PHE A 640 TYR 0.016 0.001 TYR E 828 ARG 0.013 0.001 ARG A 909 *********************** 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 224 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.7210 (tmm) cc_final: 0.6910 (tmm) REVERT: A 809 MET cc_start: 0.7802 (mpp) cc_final: 0.7091 (mpp) REVERT: A 857 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7057 (mm-30) REVERT: M 84 MET cc_start: 0.3832 (mtt) cc_final: 0.3492 (mtt) REVERT: M 294 PHE cc_start: 0.5751 (m-80) cc_final: 0.5450 (m-10) REVERT: E 547 MET cc_start: 0.7171 (tmm) cc_final: 0.6853 (tmm) REVERT: E 857 GLU cc_start: 0.7697 (pp20) cc_final: 0.7428 (pp20) REVERT: E 939 LYS cc_start: 0.8366 (tppt) cc_final: 0.7872 (tppt) REVERT: E 995 ARG cc_start: 0.7533 (mmm160) cc_final: 0.6546 (mmm-85) REVERT: N 84 MET cc_start: 0.3997 (mtt) cc_final: 0.3636 (mtt) REVERT: N 273 MET cc_start: 0.4679 (tpp) cc_final: 0.4259 (tpp) REVERT: N 294 PHE cc_start: 0.5835 (m-80) cc_final: 0.5514 (m-10) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2781 time to fit residues: 92.7270 Evaluate side-chains 168 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 175 optimal weight: 0.0070 overall best weight: 2.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 340 HIS M 361 ASN E1032 ASN ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16736 Z= 0.223 Angle : 0.728 8.891 23086 Z= 0.385 Chirality : 0.043 0.201 2612 Planarity : 0.005 0.080 2616 Dihedral : 20.933 176.396 3052 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.89 % Favored : 83.11 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.19), residues: 1788 helix: 0.83 (0.25), residues: 432 sheet: -0.78 (0.35), residues: 210 loop : -3.91 (0.15), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP N 226 HIS 0.005 0.001 HIS A 693 PHE 0.015 0.001 PHE E 640 TYR 0.018 0.001 TYR N 199 ARG 0.012 0.001 ARG A 909 *********************** 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 219 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.621 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: 0.7050 (tmm) cc_final: 0.6622 (tmm) REVERT: A 809 MET cc_start: 0.7675 (mpp) cc_final: 0.7082 (mpp) REVERT: M 294 PHE cc_start: 0.5803 (m-80) cc_final: 0.5481 (m-10) REVERT: E 547 MET cc_start: 0.7584 (tmm) cc_final: 0.6905 (tmm) REVERT: E 939 LYS cc_start: 0.8384 (tppt) cc_final: 0.7981 (tppt) REVERT: N 294 PHE cc_start: 0.5944 (m-80) cc_final: 0.5523 (m-10) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2792 time to fit residues: 91.1753 Evaluate side-chains 166 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 20.0000 chunk 170 optimal weight: 0.0170 chunk 175 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 963 HIS ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 963 HIS ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16736 Z= 0.251 Angle : 0.747 9.495 23086 Z= 0.397 Chirality : 0.044 0.218 2612 Planarity : 0.005 0.064 2616 Dihedral : 20.944 175.468 3052 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.40 % Favored : 81.60 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.19), residues: 1788 helix: 0.73 (0.25), residues: 446 sheet: -0.71 (0.35), residues: 210 loop : -3.97 (0.15), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 226 HIS 0.005 0.001 HIS E 693 PHE 0.015 0.002 PHE E 640 TYR 0.022 0.001 TYR E 828 ARG 0.005 0.001 ARG A 956 *********************** 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 215 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.828 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: A 547 MET cc_start: 0.7034 (tmm) cc_final: 0.6528 (tmm) REVERT: A 560 LEU cc_start: 0.9090 (mt) cc_final: 0.8570 (tp) REVERT: A 809 MET cc_start: 0.7876 (mpp) cc_final: 0.7281 (mpp) REVERT: M 294 PHE cc_start: 0.5838 (m-80) cc_final: 0.5544 (m-10) REVERT: E 547 MET cc_start: 0.7383 (tmm) cc_final: 0.6572 (tmm) REVERT: E 939 LYS cc_start: 0.8353 (tppt) cc_final: 0.7871 (tppt) REVERT: N 294 PHE cc_start: 0.5910 (m-80) cc_final: 0.5648 (m-10) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2685 time to fit residues: 86.6304 Evaluate side-chains 167 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 ASN ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16736 Z= 0.335 Angle : 0.819 9.572 23086 Z= 0.435 Chirality : 0.046 0.215 2612 Planarity : 0.006 0.062 2616 Dihedral : 21.129 175.012 3052 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.02 % Favored : 80.98 % 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 : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.18), residues: 1788 helix: 0.52 (0.25), residues: 440 sheet: -0.69 (0.37), residues: 190 loop : -4.09 (0.15), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP N 226 HIS 0.006 0.001 HIS A1076 PHE 0.015 0.002 PHE A 873 TYR 0.024 0.002 TYR E 828 ARG 0.006 0.001 ARG A 956 ********************** 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 203 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.685 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: 0.7237 (tmm) cc_final: 0.6702 (tmm) REVERT: A 560 LEU cc_start: 0.9037 (mt) cc_final: 0.8625 (tp) REVERT: M 294 PHE cc_start: 0.6138 (m-80) cc_final: 0.5453 (m-80) REVERT: E 547 MET cc_start: 0.7337 (tmm) cc_final: 0.6450 (tmm) REVERT: E 939 LYS cc_start: 0.8404 (tppt) cc_final: 0.7883 (tppt) REVERT: N 289 LEU cc_start: 0.7642 (mt) cc_final: 0.7285 (mp) REVERT: N 294 PHE cc_start: 0.6139 (m-80) cc_final: 0.5919 (m-10) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2795 time to fit residues: 85.4150 Evaluate side-chains 165 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 27 optimal weight: 0.0270 chunk 132 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.110288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.091105 restraints weight = 54524.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.093792 restraints weight = 33349.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.095645 restraints weight = 23175.943| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16736 Z= 0.202 Angle : 0.724 9.718 23086 Z= 0.386 Chirality : 0.043 0.220 2612 Planarity : 0.005 0.055 2616 Dihedral : 20.862 174.493 3052 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.78 % Favored : 83.22 % 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 : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.19), residues: 1788 helix: 0.90 (0.25), residues: 446 sheet: -0.42 (0.38), residues: 188 loop : -3.96 (0.15), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP N 226 HIS 0.008 0.001 HIS A 693 PHE 0.016 0.002 PHE E 640 TYR 0.020 0.001 TYR E 828 ARG 0.005 0.000 ARG M 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3002.74 seconds wall clock time: 55 minutes 25.48 seconds (3325.48 seconds total)