Starting phenix.real_space_refine on Fri Sep 27 12:42:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b40_7046/09_2024/6b40_7046.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b40_7046/09_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_7046/09_2024/6b40_7046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b40_7046/09_2024/6b40_7046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b40_7046/09_2024/6b40_7046.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b40_7046/09_2024/6b40_7046.cif" } 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. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: F, H, E, N, G Time building chain proxies: 12.37, per 1000 atoms: 0.76 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: 4.05 Conformation dependent library (CDL) restraints added in 1.7 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: 5.10 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: 5.41 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3765 1.33 - 1.45: 3795 1.45 - 1.57: 8808 1.57 - 1.69: 194 1.69 - 1.81: 172 Bond restraints: 16734 Sorted by residual: bond pdb=" C TYR E 878 " pdb=" N PRO E 879 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.19e+00 bond pdb=" C TYR A 878 " pdb=" N PRO A 879 " ideal model delta sigma weight residual 1.334 1.381 -0.048 2.34e-02 1.83e+03 4.13e+00 bond pdb=" CB ILE M 172 " pdb=" CG2 ILE M 172 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" CB ILE N 172 " pdb=" CG2 ILE N 172 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" C ASP E 684 " pdb=" N PRO E 685 " ideal model delta sigma weight residual 1.340 1.394 -0.054 2.76e-02 1.31e+03 3.83e+00 ... (remaining 16729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 22597 3.29 - 6.57: 437 6.57 - 9.86: 40 9.86 - 13.15: 2 13.15 - 16.43: 4 Bond angle restraints: 23080 Sorted by residual: angle pdb=" C ASN A 747 " pdb=" N PRO A 748 " pdb=" CD PRO A 748 " ideal model delta sigma weight residual 120.60 104.17 16.43 2.20e+00 2.07e-01 5.58e+01 angle pdb=" C ASN E 747 " pdb=" N PRO E 748 " pdb=" CD PRO E 748 " ideal model delta sigma weight residual 120.60 104.18 16.42 2.20e+00 2.07e-01 5.57e+01 angle pdb=" C ASN E 747 " pdb=" N PRO E 748 " pdb=" CA PRO E 748 " ideal model delta sigma weight residual 127.00 140.99 -13.99 2.40e+00 1.74e-01 3.40e+01 angle pdb=" C ASN A 747 " pdb=" N PRO A 748 " pdb=" CA PRO A 748 " ideal model delta sigma weight residual 127.00 140.97 -13.97 2.40e+00 1.74e-01 3.39e+01 angle pdb=" N LEU N 173 " pdb=" CA LEU N 173 " pdb=" C LEU N 173 " ideal model delta sigma weight residual 109.24 116.68 -7.44 1.67e+00 3.59e-01 1.98e+01 ... (remaining 23075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 9430 34.43 - 68.86: 450 68.86 - 103.29: 12 103.29 - 137.72: 0 137.72 - 172.15: 4 Dihedral angle restraints: 9896 sinusoidal: 4572 harmonic: 5324 Sorted by residual: dihedral pdb=" CA THR A 882 " pdb=" C THR A 882 " pdb=" N THR A 883 " pdb=" CA THR A 883 " ideal model delta harmonic sigma weight residual 180.00 -136.00 -44.00 0 5.00e+00 4.00e-02 7.74e+01 dihedral pdb=" CA THR E 882 " pdb=" C THR E 882 " pdb=" N THR E 883 " pdb=" CA THR E 883 " ideal model delta harmonic sigma weight residual 180.00 -136.01 -43.99 0 5.00e+00 4.00e-02 7.74e+01 dihedral pdb=" CA UNK E1119 " pdb=" C UNK E1119 " pdb=" N UNK E1120 " pdb=" CA UNK E1120 " ideal model delta harmonic sigma weight residual 180.00 141.49 38.51 0 5.00e+00 4.00e-02 5.93e+01 ... (remaining 9893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1586 0.046 - 0.091: 729 0.091 - 0.137: 225 0.137 - 0.182: 54 0.182 - 0.228: 18 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CB ILE E 695 " pdb=" CA ILE E 695 " pdb=" CG1 ILE E 695 " pdb=" CG2 ILE E 695 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE N 172 " pdb=" N ILE N 172 " pdb=" C ILE N 172 " pdb=" CB ILE N 172 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE A 695 " pdb=" CA ILE A 695 " pdb=" CG1 ILE A 695 " pdb=" CG2 ILE A 695 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2609 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 747 " -0.048 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO A 748 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 748 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 748 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 747 " -0.048 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO E 748 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 748 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 748 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 135 " 0.047 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO N 136 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO N 136 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 136 " 0.039 5.00e-02 4.00e+02 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3920 2.79 - 3.32: 14738 3.32 - 3.85: 27250 3.85 - 4.37: 29910 4.37 - 4.90: 47521 Nonbonded interactions: 123339 Sorted by model distance: nonbonded pdb=" NZ LYS A 563 " pdb=" OP2 DA G 8 " model vdw 2.269 3.120 nonbonded pdb=" OD2 ASP A 891 " pdb=" OG SER A1059 " model vdw 2.279 3.040 nonbonded pdb=" OD2 ASP E 891 " pdb=" OG SER E1059 " model vdw 2.279 3.040 nonbonded pdb=" OG SER M 284 " pdb=" O GLY M 298 " model vdw 2.281 3.040 nonbonded pdb=" OG SER N 284 " pdb=" O GLY N 298 " model vdw 2.281 3.040 ... (remaining 123334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 44.730 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.210 ------------------------------------------------------------------------------- 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 16734 Z= 0.467 Angle : 1.128 16.433 23080 Z= 0.622 Chirality : 0.059 0.228 2612 Planarity : 0.008 0.090 2614 Dihedral : 16.851 172.154 6454 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 18.79 % Favored : 80.98 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.24 % Rama-Z (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 : 1.657 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: 0.3376 time to fit residues: 185.3238 Evaluate side-chains 211 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 147 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 GLN A 792 HIS A 915 HIS A1042 GLN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 780 GLN E 792 HIS E 915 HIS E1042 GLN ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16734 Z= 0.386 Angle : 0.911 10.312 23080 Z= 0.484 Chirality : 0.049 0.196 2612 Planarity : 0.007 0.068 2614 Dihedral : 21.829 177.280 3050 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 17.90 % Favored : 81.88 % Rotamer: Outliers : 0.19 % Allowed : 2.17 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.24 % Rama-Z (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: -4.50 (0.17), residues: 1788 helix: -0.88 (0.23), residues: 434 sheet: -2.01 (0.36), residues: 190 loop : -4.34 (0.14), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 917 HIS 0.009 0.002 HIS N 161 PHE 0.014 0.002 PHE N 52 TYR 0.027 0.002 TYR A 828 ARG 0.006 0.001 ARG E 755 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 263 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 GLU cc_start: 0.7637 (pt0) cc_final: 0.6966 (tt0) REVERT: A 734 MET cc_start: 0.1281 (ptp) cc_final: 0.0404 (tpt) REVERT: A 816 ARG cc_start: 0.8485 (mtp85) cc_final: 0.8267 (mtp85) REVERT: A 847 TYR cc_start: 0.7084 (m-80) cc_final: 0.6458 (m-80) REVERT: A 1053 SER cc_start: 0.8409 (p) cc_final: 0.8189 (m) REVERT: M 106 ASP cc_start: 0.5882 (t70) cc_final: 0.5654 (m-30) REVERT: M 233 MET cc_start: 0.5607 (tpt) cc_final: 0.4551 (tpt) REVERT: E 711 GLU cc_start: 0.7728 (pt0) cc_final: 0.7490 (tt0) REVERT: E 847 TYR cc_start: 0.6854 (m-80) cc_final: 0.6192 (m-80) REVERT: E 939 LYS cc_start: 0.8616 (tppt) cc_final: 0.8108 (tppt) REVERT: E 1034 LEU cc_start: 0.8711 (mp) cc_final: 0.8150 (tt) REVERT: N 234 VAL cc_start: 0.7732 (t) cc_final: 0.7255 (p) outliers start: 3 outliers final: 0 residues processed: 265 average time/residue: 0.3075 time to fit residues: 116.9606 Evaluate side-chains 178 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** A1042 GLN ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 HIS ** M 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1042 GLN ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 ASN N 329 HIS ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16734 Z= 0.264 Angle : 0.788 7.816 23080 Z= 0.425 Chirality : 0.045 0.226 2612 Planarity : 0.006 0.058 2614 Dihedral : 21.411 174.791 3050 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 17.51 % Favored : 82.27 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -4.16 (0.18), residues: 1788 helix: -0.38 (0.24), residues: 434 sheet: -2.00 (0.34), residues: 200 loop : -4.19 (0.15), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 917 HIS 0.007 0.001 HIS M 161 PHE 0.015 0.002 PHE M 52 TYR 0.027 0.002 TYR A 828 ARG 0.007 0.001 ARG E1102 *********************** 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 243 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.684 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: 0.8035 (tt0) cc_final: 0.7614 (tm-30) REVERT: A 711 GLU cc_start: 0.7664 (pt0) cc_final: 0.7402 (tt0) REVERT: A 734 MET cc_start: 0.1693 (ptp) cc_final: 0.1053 (tpt) REVERT: M 233 MET cc_start: 0.5797 (tpt) cc_final: 0.4143 (tpt) REVERT: E 668 GLU cc_start: 0.8014 (tt0) cc_final: 0.7703 (tm-30) REVERT: E 711 GLU cc_start: 0.7853 (pt0) cc_final: 0.7495 (tt0) REVERT: E 816 ARG cc_start: 0.8343 (mtp85) cc_final: 0.8051 (mtp85) REVERT: E 858 VAL cc_start: 0.8167 (m) cc_final: 0.7792 (m) REVERT: E 939 LYS cc_start: 0.8558 (tppt) cc_final: 0.8044 (tptt) REVERT: E 1038 ILE cc_start: 0.8886 (pt) cc_final: 0.8583 (mt) REVERT: N 303 ASP cc_start: 0.6401 (p0) cc_final: 0.6115 (p0) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2930 time to fit residues: 103.5677 Evaluate side-chains 174 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 9.9990 chunk 128 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 0.0000 chunk 81 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 overall best weight: 2.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1024 HIS ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16734 Z= 0.262 Angle : 0.771 8.559 23080 Z= 0.415 Chirality : 0.045 0.216 2612 Planarity : 0.006 0.092 2614 Dihedral : 21.380 176.261 3050 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.56 % Favored : 82.44 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.24 % Rama-Z (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: -3.93 (0.18), residues: 1788 helix: -0.05 (0.25), residues: 440 sheet: -1.88 (0.34), residues: 204 loop : -4.12 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 917 HIS 0.011 0.001 HIS M 161 PHE 0.012 0.002 PHE A 640 TYR 0.026 0.002 TYR A 828 ARG 0.011 0.001 ARG E 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 230 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.882 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: 0.1521 (ptp) cc_final: 0.0656 (tpt) REVERT: M 84 MET cc_start: 0.3914 (mtt) cc_final: 0.3595 (mtt) REVERT: M 233 MET cc_start: 0.5805 (tpt) cc_final: 0.4683 (tpt) REVERT: E 761 ILE cc_start: 0.8609 (mt) cc_final: 0.8367 (mt) REVERT: E 816 ARG cc_start: 0.8310 (mtp85) cc_final: 0.8075 (mtp85) REVERT: E 858 VAL cc_start: 0.8199 (m) cc_final: 0.7817 (m) REVERT: E 939 LYS cc_start: 0.8488 (tppt) cc_final: 0.7967 (tppt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3048 time to fit residues: 103.0656 Evaluate side-chains 168 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 HIS ** 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** N 47 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16734 Z= 0.307 Angle : 0.805 9.053 23080 Z= 0.431 Chirality : 0.046 0.229 2612 Planarity : 0.006 0.095 2614 Dihedral : 21.509 175.737 3050 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 18.68 % Favored : 81.21 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -3.87 (0.18), residues: 1788 helix: -0.10 (0.24), residues: 446 sheet: -1.88 (0.34), residues: 224 loop : -4.08 (0.16), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 917 HIS 0.007 0.001 HIS M 161 PHE 0.011 0.002 PHE A 640 TYR 0.021 0.002 TYR A 828 ARG 0.006 0.001 ARG A 995 *********************** 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 218 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.811 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 734 MET cc_start: 0.1856 (ptp) cc_final: 0.0698 (tpt) REVERT: A 809 MET cc_start: 0.7906 (mpp) cc_final: 0.7441 (mpp) REVERT: M 84 MET cc_start: 0.3930 (mtt) cc_final: 0.3603 (mtt) REVERT: M 233 MET cc_start: 0.6196 (tpt) cc_final: 0.5025 (tpt) REVERT: E 809 MET cc_start: 0.7878 (mpp) cc_final: 0.7471 (mpp) REVERT: E 858 VAL cc_start: 0.8206 (m) cc_final: 0.7807 (m) REVERT: E 939 LYS cc_start: 0.8568 (tppt) cc_final: 0.7939 (tppt) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2845 time to fit residues: 92.3398 Evaluate side-chains 163 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.0030 chunk 95 optimal weight: 7.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1042 GLN ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16734 Z= 0.291 Angle : 0.791 9.991 23080 Z= 0.424 Chirality : 0.046 0.245 2612 Planarity : 0.006 0.100 2614 Dihedral : 21.449 175.247 3050 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 17.90 % Favored : 82.05 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -3.78 (0.18), residues: 1788 helix: 0.05 (0.24), residues: 446 sheet: -1.46 (0.37), residues: 194 loop : -4.09 (0.15), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP M 208 HIS 0.007 0.001 HIS E 641 PHE 0.013 0.002 PHE A 640 TYR 0.017 0.002 TYR A 828 ARG 0.013 0.001 ARG A 909 *********************** 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 208 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.775 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 734 MET cc_start: 0.1761 (ptp) cc_final: 0.0600 (tpt) REVERT: A 995 ARG cc_start: 0.7696 (mmm160) cc_final: 0.7329 (mmm160) REVERT: M 84 MET cc_start: 0.4319 (mtt) cc_final: 0.4023 (mtt) REVERT: M 233 MET cc_start: 0.6089 (tpt) cc_final: 0.5057 (tpt) REVERT: E 858 VAL cc_start: 0.8221 (m) cc_final: 0.7842 (m) REVERT: E 939 LYS cc_start: 0.8574 (tppt) cc_final: 0.7958 (tppt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2745 time to fit residues: 85.8396 Evaluate side-chains 158 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 181 optimal weight: 0.0170 chunk 113 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 83 optimal weight: 0.0980 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 HIS ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1042 GLN ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 GLN N 340 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16734 Z= 0.195 Angle : 0.718 8.573 23080 Z= 0.386 Chirality : 0.044 0.224 2612 Planarity : 0.005 0.103 2614 Dihedral : 21.106 174.786 3050 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.88 % Favored : 84.12 % 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 : 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: -3.41 (0.19), residues: 1788 helix: 0.56 (0.25), residues: 438 sheet: -0.97 (0.37), residues: 194 loop : -3.98 (0.15), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 886 HIS 0.006 0.001 HIS E 693 PHE 0.013 0.001 PHE A 640 TYR 0.023 0.001 TYR M 199 ARG 0.008 0.000 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 229 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.744 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 734 MET cc_start: 0.1321 (ptp) cc_final: 0.0841 (tpt) REVERT: A 995 ARG cc_start: 0.7553 (mmm160) cc_final: 0.7021 (tpp80) REVERT: M 84 MET cc_start: 0.4010 (mtt) cc_final: 0.3685 (mtt) REVERT: E 939 LYS cc_start: 0.8385 (tppt) cc_final: 0.7890 (tppt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2654 time to fit residues: 91.9475 Evaluate side-chains 181 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** A 963 HIS ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 GLN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 HIS ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16734 Z= 0.382 Angle : 0.856 9.714 23080 Z= 0.454 Chirality : 0.048 0.305 2612 Planarity : 0.006 0.107 2614 Dihedral : 21.420 178.223 3050 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 19.02 % Favored : 80.93 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: -3.73 (0.18), residues: 1788 helix: 0.13 (0.24), residues: 438 sheet: -1.18 (0.38), residues: 192 loop : -4.10 (0.15), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 886 HIS 0.006 0.002 HIS A1076 PHE 0.013 0.002 PHE E 873 TYR 0.019 0.002 TYR E 994 ARG 0.005 0.001 ARG A 888 *********************** 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 201 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.800 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 734 MET cc_start: 0.1983 (ptp) cc_final: 0.0518 (tpt) REVERT: A 809 MET cc_start: 0.7852 (mpp) cc_final: 0.7511 (mpp) REVERT: A 815 ASP cc_start: 0.8060 (t0) cc_final: 0.7840 (t70) REVERT: A 995 ARG cc_start: 0.7559 (mmm160) cc_final: 0.7230 (mmm160) REVERT: M 233 MET cc_start: 0.5952 (tpt) cc_final: 0.5344 (tpt) REVERT: E 939 LYS cc_start: 0.8621 (tppt) cc_final: 0.8195 (tppt) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2646 time to fit residues: 80.9688 Evaluate side-chains 163 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.0770 chunk 158 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 101 optimal weight: 0.3980 chunk 73 optimal weight: 0.0870 chunk 132 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 HIS ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16734 Z= 0.194 Angle : 0.735 8.557 23080 Z= 0.390 Chirality : 0.044 0.226 2612 Planarity : 0.005 0.085 2614 Dihedral : 21.030 175.123 3050 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.16 % Favored : 84.84 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (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: -3.26 (0.19), residues: 1788 helix: 0.73 (0.25), residues: 426 sheet: -0.52 (0.38), residues: 188 loop : -3.91 (0.15), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 886 HIS 0.008 0.001 HIS E 693 PHE 0.012 0.001 PHE A 640 TYR 0.016 0.001 TYR A 828 ARG 0.007 0.000 ARG A 909 *********************** 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 231 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.638 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 734 MET cc_start: 0.1367 (ptp) cc_final: 0.0840 (tpt) REVERT: A 809 MET cc_start: 0.7779 (mpp) cc_final: 0.6728 (mpp) REVERT: A 1003 MET cc_start: 0.6225 (mmm) cc_final: 0.5924 (mmm) REVERT: E 638 MET cc_start: 0.7365 (mtm) cc_final: 0.7069 (mtp) REVERT: E 939 LYS cc_start: 0.8370 (tppt) cc_final: 0.7847 (tppt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2521 time to fit residues: 88.5872 Evaluate side-chains 172 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 187 optimal weight: 0.0670 chunk 172 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16734 Z= 0.214 Angle : 0.741 8.664 23080 Z= 0.392 Chirality : 0.045 0.289 2612 Planarity : 0.005 0.095 2614 Dihedral : 21.013 176.891 3050 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.94 % Favored : 84.06 % 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 : 0.12 % 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: -3.22 (0.19), residues: 1788 helix: 0.72 (0.25), residues: 426 sheet: -0.30 (0.39), residues: 188 loop : -3.90 (0.15), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP N 226 HIS 0.004 0.001 HIS A 693 PHE 0.014 0.001 PHE A 640 TYR 0.020 0.001 TYR N 197 ARG 0.006 0.000 ARG A 909 ********************** 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 210 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.738 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 734 MET cc_start: 0.1390 (ptp) cc_final: 0.0549 (tpt) REVERT: A 809 MET cc_start: 0.7620 (mpp) cc_final: 0.6913 (mpp) REVERT: M 145 ILE cc_start: 0.8290 (mp) cc_final: 0.8085 (mt) REVERT: M 304 LYS cc_start: 0.7138 (ptpt) cc_final: 0.6872 (ptpt) REVERT: E 560 LEU cc_start: 0.8955 (mt) cc_final: 0.8699 (tp) REVERT: E 667 LEU cc_start: 0.8278 (pp) cc_final: 0.8077 (tp) REVERT: E 857 GLU cc_start: 0.7901 (pp20) cc_final: 0.7682 (pp20) REVERT: E 939 LYS cc_start: 0.8422 (tppt) cc_final: 0.7894 (tppt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2583 time to fit residues: 83.5256 Evaluate side-chains 172 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.7603 > 50: distance: 26 - 88: 29.047 distance: 29 - 85: 29.143 distance: 53 - 58: 29.362 distance: 58 - 59: 3.256 distance: 59 - 60: 40.539 distance: 59 - 62: 54.189 distance: 60 - 61: 39.175 distance: 60 - 65: 32.247 distance: 62 - 63: 19.703 distance: 62 - 64: 44.938 distance: 65 - 66: 39.705 distance: 65 - 204: 34.151 distance: 66 - 67: 32.049 distance: 66 - 69: 4.612 distance: 67 - 68: 40.409 distance: 67 - 74: 5.881 distance: 68 - 201: 32.087 distance: 69 - 70: 15.947 distance: 70 - 71: 18.582 distance: 71 - 72: 60.786 distance: 72 - 73: 18.905 distance: 74 - 75: 57.026 distance: 75 - 76: 40.229 distance: 76 - 77: 45.255 distance: 76 - 78: 37.068 distance: 78 - 79: 35.744 distance: 78 - 192: 24.369 distance: 79 - 80: 21.070 distance: 79 - 82: 48.704 distance: 80 - 81: 6.608 distance: 80 - 85: 43.878 distance: 81 - 189: 30.393 distance: 82 - 83: 31.115 distance: 82 - 84: 21.019 distance: 85 - 86: 47.014 distance: 86 - 87: 57.969 distance: 86 - 89: 39.595 distance: 87 - 88: 12.581 distance: 87 - 96: 39.661 distance: 89 - 90: 41.334 distance: 92 - 93: 19.224 distance: 93 - 94: 30.564 distance: 93 - 95: 13.820 distance: 96 - 97: 40.400 distance: 97 - 98: 44.007 distance: 97 - 100: 9.385 distance: 98 - 99: 36.202 distance: 98 - 107: 20.206 distance: 100 - 101: 52.292 distance: 101 - 102: 43.653 distance: 101 - 103: 40.618 distance: 102 - 104: 24.758 distance: 103 - 105: 39.100 distance: 104 - 106: 54.310 distance: 105 - 106: 39.995 distance: 107 - 108: 21.500 distance: 107 - 113: 40.069 distance: 108 - 109: 20.884 distance: 108 - 111: 33.013 distance: 109 - 110: 22.738 distance: 109 - 114: 29.379 distance: 110 - 141: 29.182 distance: 111 - 112: 27.837 distance: 112 - 113: 46.897 distance: 114 - 115: 29.754 distance: 115 - 116: 23.484 distance: 115 - 118: 11.690 distance: 116 - 117: 20.661 distance: 116 - 126: 12.451 distance: 117 - 146: 31.271 distance: 118 - 119: 31.367 distance: 119 - 120: 19.527 distance: 119 - 121: 17.466 distance: 120 - 122: 30.478 distance: 121 - 123: 25.165 distance: 122 - 124: 32.681 distance: 123 - 124: 33.078 distance: 124 - 125: 8.466 distance: 126 - 127: 10.744 distance: 127 - 128: 34.857 distance: 127 - 130: 28.583 distance: 128 - 129: 38.939 distance: 129 - 153: 35.666 distance: 131 - 132: 28.536 distance: 132 - 133: 12.030 distance: 132 - 135: 40.595 distance: 133 - 134: 31.592 distance: 133 - 141: 13.218 distance: 134 - 158: 35.550 distance: 135 - 136: 27.616 distance: 136 - 137: 24.448 distance: 136 - 138: 61.249 distance: 137 - 139: 5.915 distance: 138 - 140: 14.689 distance: 139 - 140: 42.369