Starting phenix.real_space_refine on Thu Aug 6 11:53:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tih_55956/08_2026/9tih_55956.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tih_55956/08_2026/9tih_55956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tih_55956/08_2026/9tih_55956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tih_55956/08_2026/9tih_55956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tih_55956/08_2026/9tih_55956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tih_55956/08_2026/9tih_55956.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 9327 2.51 5 N 2382 2.21 5 O 2960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14699 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2695 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 17, 'TRANS': 324} Chain breaks: 2 Chain: "B" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1327 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "C" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1033 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Chain breaks: 2 Chain: "D" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1314 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 8, 'TRANS': 157} Chain: "E" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1349 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "F" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1272 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain breaks: 1 Chain: "G" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2142 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain breaks: 2 Chain: "H" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1157 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 5 Chain: "I" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1259 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "J" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 2 Time building chain proxies: 3.15, per 1000 atoms: 0.21 Number of scatterers: 14699 At special positions: 0 Unit cell: (143.379, 140.045, 128.374, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 2960 8.00 N 2382 7.00 C 9327 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 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 654.4 milliseconds 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3458 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 35 sheets defined 12.7% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 15 through 18 Processing helix chain 'A' and resid 32 through 55 removed outlier: 3.637A pdb=" N LEU A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 4.690A pdb=" N ALA A 121 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER A 122 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.551A pdb=" N LYS A 136 " --> pdb=" O TYR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'B' and resid 15 through 18 Processing helix chain 'B' and resid 32 through 55 removed outlier: 4.158A pdb=" N LEU B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.532A pdb=" N LEU B 124 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'D' and resid 15 through 18 Processing helix chain 'D' and resid 32 through 53 removed outlier: 3.924A pdb=" N LEU D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'E' and resid 5 through 18 removed outlier: 3.645A pdb=" N HIS E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 22 Processing helix chain 'E' and resid 68 through 73 removed outlier: 3.907A pdb=" N ASP E 73 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'F' and resid 5 through 19 removed outlier: 4.075A pdb=" N HIS F 9 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS F 19 " --> pdb=" O TYR F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 138 through 140 No H-bonds generated for 'chain 'F' and resid 138 through 140' Processing helix chain 'G' and resid 290 through 296 removed outlier: 4.118A pdb=" N TYR G 294 " --> pdb=" O PRO G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 332 Processing helix chain 'G' and resid 341 through 351 removed outlier: 3.665A pdb=" N LYS G 351 " --> pdb=" O SER G 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 52 removed outlier: 3.848A pdb=" N SER H 51 " --> pdb=" O ASN H 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 51 Processing helix chain 'I' and resid 129 through 133 Processing helix chain 'I' and resid 148 through 151 Processing helix chain 'J' and resid 47 through 51 Processing helix chain 'J' and resid 129 through 133 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 24 removed outlier: 3.821A pdb=" N LYS A 22 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.313A pdb=" N LYS A 60 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR A 82 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 62 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 69 Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 165 removed outlier: 5.900A pdb=" N THR A 156 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 108 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 158 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS D 22 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLU A 143 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG D 20 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 569 through 573 removed outlier: 6.859A pdb=" N ILE A 938 " --> pdb=" O THR A 571 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 808 " --> pdb=" O TYR A 939 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 869 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N SER A 808 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 12.366A pdb=" N ASP A 867 " --> pdb=" O SER A 808 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 582 removed outlier: 6.175A pdb=" N THR A 889 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 579 through 582 Processing sheet with id=AA8, first strand: chain 'A' and resid 836 through 847 removed outlier: 7.977A pdb=" N ILE A 840 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLY A 829 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 842 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET A 830 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU A 876 " --> pdb=" O MET A 830 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 917 " --> pdb=" O HIS A 929 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 897 through 899 removed outlier: 4.125A pdb=" N LYS A 897 " --> pdb=" O ILE A 907 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLU A 905 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 20 through 24 removed outlier: 3.974A pdb=" N LYS B 22 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 59 through 63 removed outlier: 4.009A pdb=" N ASP B 59 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR B 80 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 79 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 81 " --> pdb=" O ARG B 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AB4, first strand: chain 'B' and resid 148 through 149 removed outlier: 6.926A pdb=" N ILE B 108 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR B 156 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.692A pdb=" N GLY C 54 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET C 124 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU C 148 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 78 through 80 removed outlier: 7.305A pdb=" N SER C 84 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 67 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 60 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR F 164 " --> pdb=" O PHE G 203 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP F 100 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS F 60 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU F 63 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER F 84 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 78 through 80 removed outlier: 7.305A pdb=" N SER C 84 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 67 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 60 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR F 164 " --> pdb=" O PHE G 203 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR G 207 " --> pdb=" O LYS F 166 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG F 168 " --> pdb=" O THR G 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 62 through 63 removed outlier: 4.177A pdb=" N SER D 62 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AC1, first strand: chain 'D' and resid 145 through 149 removed outlier: 3.682A pdb=" N TYR D 158 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE D 108 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR D 156 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.673A pdb=" N PHE F 151 " --> pdb=" O ILE E 3 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU F 148 " --> pdb=" O MET F 124 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N MET F 124 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE F 150 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE F 27 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY F 54 " --> pdb=" O ILE F 27 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 52 through 57 removed outlier: 6.840A pdb=" N ILE E 27 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR E 55 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU E 25 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR E 24 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL E 120 " --> pdb=" O PHE E 151 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE E 151 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE E 122 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 77 through 80 removed outlier: 3.820A pdb=" N LEU E 63 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP E 100 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL E 101 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL E 171 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 127 through 128 removed outlier: 4.209A pdb=" N VAL E 127 " --> pdb=" O SER E 144 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER E 144 " --> pdb=" O VAL E 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AC7, first strand: chain 'G' and resid 216 through 217 Processing sheet with id=AC8, first strand: chain 'G' and resid 216 through 217 removed outlier: 5.198A pdb=" N VAL G 433 " --> pdb=" O SER G 360 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER G 360 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR G 435 " --> pdb=" O TYR G 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 287 through 288 removed outlier: 5.805A pdb=" N PHE G 416 " --> pdb=" O TYR G 376 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU G 370 " --> pdb=" O ASN G 422 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE G 369 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASN G 390 " --> pdb=" O ILE G 369 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE G 371 " --> pdb=" O ILE G 388 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE G 388 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU G 373 " --> pdb=" O VAL G 386 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 38 through 41 removed outlier: 3.972A pdb=" N LYS H 38 " --> pdb=" O ASN H 57 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR H 61 " --> pdb=" O ILE H 40 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP H 79 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS H 87 " --> pdb=" O ASP H 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 137 through 141 removed outlier: 3.511A pdb=" N GLY H 154 " --> pdb=" O ALA H 141 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 39 through 41 removed outlier: 3.832A pdb=" N THR I 61 " --> pdb=" O ILE I 40 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR I 85 " --> pdb=" O ARG I 81 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR I 86 " --> pdb=" O TYR I 103 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 39 through 41 removed outlier: 3.832A pdb=" N THR I 61 " --> pdb=" O ILE I 40 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR I 85 " --> pdb=" O ARG I 81 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR I 86 " --> pdb=" O TYR I 103 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE I 112 " --> pdb=" O ILE I 100 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 124 through 128 removed outlier: 4.592A pdb=" N GLU I 124 " --> pdb=" O TYR I 140 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR I 142 " --> pdb=" O GLU I 124 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN I 126 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N SER I 178 " --> pdb=" O PRO I 173 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 58 through 60 removed outlier: 3.563A pdb=" N TYR J 58 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL J 60 " --> pdb=" O GLY J 74 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY J 74 " --> pdb=" O VAL J 60 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG J 77 " --> pdb=" O TYR J 89 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 58 through 60 removed outlier: 3.563A pdb=" N TYR J 58 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL J 60 " --> pdb=" O GLY J 74 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY J 74 " --> pdb=" O VAL J 60 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG J 77 " --> pdb=" O TYR J 89 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 124 through 128 removed outlier: 6.484A pdb=" N GLU J 124 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TYR J 140 " --> pdb=" O GLU J 124 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN J 126 " --> pdb=" O TYR J 140 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY J 154 " --> pdb=" O ALA J 141 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4723 1.34 - 1.46: 3032 1.46 - 1.57: 7185 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 15000 Sorted by residual: bond pdb=" CA VAL B 73 " pdb=" CB VAL B 73 " ideal model delta sigma weight residual 1.527 1.540 -0.014 1.31e-02 5.83e+03 1.06e+00 bond pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.05e+00 bond pdb=" CA ILE A 167 " pdb=" CB ILE A 167 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.01e+00 bond pdb=" CA GLN H 42 " pdb=" CB GLN H 42 " ideal model delta sigma weight residual 1.522 1.529 -0.007 7.00e-03 2.04e+04 9.54e-01 bond pdb=" C GLU E 111 " pdb=" N LEU E 112 " ideal model delta sigma weight residual 1.327 1.337 -0.010 1.05e-02 9.07e+03 8.94e-01 ... (remaining 14995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 19555 1.10 - 2.19: 651 2.19 - 3.29: 108 3.29 - 4.39: 22 4.39 - 5.49: 4 Bond angle restraints: 20340 Sorted by residual: angle pdb=" N ILE A 157 " pdb=" CA ILE A 157 " pdb=" C ILE A 157 " ideal model delta sigma weight residual 113.71 109.60 4.11 9.50e-01 1.11e+00 1.87e+01 angle pdb=" C GLU A 70 " pdb=" CA GLU A 70 " pdb=" CB GLU A 70 " ideal model delta sigma weight residual 116.34 110.85 5.49 1.40e+00 5.10e-01 1.54e+01 angle pdb=" N LEU E 112 " pdb=" CA LEU E 112 " pdb=" C LEU E 112 " ideal model delta sigma weight residual 108.13 105.00 3.13 9.00e-01 1.23e+00 1.21e+01 angle pdb=" N ASP E 110 " pdb=" CA ASP E 110 " pdb=" CB ASP E 110 " ideal model delta sigma weight residual 114.17 110.65 3.52 1.14e+00 7.69e-01 9.54e+00 angle pdb=" N ARG J 81 " pdb=" CA ARG J 81 " pdb=" C ARG J 81 " ideal model delta sigma weight residual 112.72 108.94 3.78 1.28e+00 6.10e-01 8.71e+00 ... (remaining 20335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 8720 14.11 - 28.21: 218 28.21 - 42.32: 46 42.32 - 56.42: 12 56.42 - 70.53: 4 Dihedral angle restraints: 9000 sinusoidal: 3601 harmonic: 5399 Sorted by residual: dihedral pdb=" CA LYS J 80 " pdb=" C LYS J 80 " pdb=" N ARG J 81 " pdb=" CA ARG J 81 " ideal model delta harmonic sigma weight residual 180.00 163.55 16.45 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" N GLN F 119 " pdb=" CA GLN F 119 " pdb=" CB GLN F 119 " pdb=" CG GLN F 119 " ideal model delta sinusoidal sigma weight residual -60.00 -119.73 59.73 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET G 309 " pdb=" CG MET G 309 " pdb=" SD MET G 309 " pdb=" CE MET G 309 " ideal model delta sinusoidal sigma weight residual 180.00 120.27 59.73 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 8997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1450 0.029 - 0.058: 525 0.058 - 0.087: 75 0.087 - 0.116: 161 0.116 - 0.145: 36 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CA VAL A 130 " pdb=" N VAL A 130 " pdb=" C VAL A 130 " pdb=" CB VAL A 130 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE I 112 " pdb=" N ILE I 112 " pdb=" C ILE I 112 " pdb=" CB ILE I 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE I 40 " pdb=" N ILE I 40 " pdb=" C ILE I 40 " pdb=" CB ILE I 40 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 2244 not shown) Planarity restraints: 2623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 130 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.03e+00 pdb=" N PRO A 131 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 116 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO D 117 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 117 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 117 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 8 " 0.016 5.00e-02 4.00e+02 2.49e-02 9.89e-01 pdb=" N PRO D 9 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO D 9 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 9 " 0.014 5.00e-02 4.00e+02 ... (remaining 2620 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 186 2.62 - 3.19: 13036 3.19 - 3.76: 20546 3.76 - 4.33: 30424 4.33 - 4.90: 51660 Nonbonded interactions: 115852 Sorted by model distance: nonbonded pdb=" OG1 THR D 99 " pdb=" OE2 GLU D 104 " model vdw 2.048 3.040 nonbonded pdb=" OG1 THR B 99 " pdb=" OE2 GLU B 104 " model vdw 2.083 3.040 nonbonded pdb=" OG SER B 69 " pdb=" OD1 ASP B 71 " model vdw 2.086 3.040 nonbonded pdb=" OD1 ASP A 52 " pdb=" OH TYR A 82 " model vdw 2.093 3.040 nonbonded pdb=" O PRO I 53 " pdb=" OH TYR I 58 " model vdw 2.094 3.040 ... (remaining 115847 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 'B' and resid 4 through 168) selection = (chain 'D' and resid 4 through 168) } ncs_group { reference = (chain 'E' and (resid 4 through 67 or resid 76 through 173)) selection = chain 'F' } ncs_group { reference = (chain 'H' and (resid 46 through 92 or resid 96 through 404)) selection = (chain 'I' and (resid 46 through 64 or resid 75 through 80 or resid 84 through 9 \ 2 or resid 96 through 103 or resid 109 through 118 or resid 121 through 404)) selection = (chain 'J' and (resid 46 through 64 or resid 75 through 80 or resid 84 through 1 \ 03 or resid 109 through 118 or resid 121 through 404)) } 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.270 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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 : 0.002 0.024 15000 Z= 0.112 Angle : 0.485 5.486 20340 Z= 0.301 Chirality : 0.041 0.145 2247 Planarity : 0.003 0.036 2623 Dihedral : 7.205 70.529 5542 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.18 % Allowed : 1.75 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1789 helix: 2.29 (0.51), residues: 128 sheet: 0.86 (0.25), residues: 488 loop : 0.19 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 205 TYR 0.005 0.000 TYR A 912 PHE 0.005 0.000 PHE H 171 TRP 0.006 0.001 TRP C 33 HIS 0.001 0.000 HIS G 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.11 (15000) covalent geometry : angle 0.48495 / 0.30 (20340) hydrogen bonds : bond 0.26466 / 16.99 ( 463) hydrogen bonds : angle 9.58219 / 6.68 ( 1305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 580 time to evaluate : 0.647 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 25 PHE cc_start: 0.8792 (m-80) cc_final: 0.8480 (m-10) REVERT: A 169 SER cc_start: 0.8169 (t) cc_final: 0.7886 (p) REVERT: A 801 ASP cc_start: 0.6707 (m-30) cc_final: 0.6404 (t0) REVERT: A 850 ASP cc_start: 0.6470 (t0) cc_final: 0.6052 (t0) REVERT: A 851 ILE cc_start: 0.8641 (mt) cc_final: 0.8341 (mt) REVERT: A 869 MET cc_start: 0.8741 (tmt) cc_final: 0.8526 (tmm) REVERT: A 884 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7030 (mm-30) REVERT: B 4 ASN cc_start: 0.5453 (t0) cc_final: 0.4880 (t0) REVERT: B 13 ARG cc_start: 0.7075 (mmt-90) cc_final: 0.6420 (mtm180) REVERT: C 45 ASN cc_start: 0.6760 (m-40) cc_final: 0.6543 (m-40) REVERT: C 48 VAL cc_start: 0.6961 (p) cc_final: 0.6759 (p) REVERT: C 65 ARG cc_start: 0.7824 (ptt90) cc_final: 0.7482 (ptt90) REVERT: C 152 ASP cc_start: 0.8308 (t0) cc_final: 0.7760 (m-30) REVERT: C 169 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: D 39 MET cc_start: 0.7515 (ttp) cc_final: 0.6852 (ttp) REVERT: D 40 GLN cc_start: 0.8559 (mt0) cc_final: 0.8300 (mt0) REVERT: D 43 ASP cc_start: 0.6728 (m-30) cc_final: 0.6414 (m-30) REVERT: D 69 SER cc_start: 0.6385 (p) cc_final: 0.5623 (t) REVERT: D 106 ILE cc_start: 0.9293 (mm) cc_final: 0.9070 (mm) REVERT: D 120 ASP cc_start: 0.8425 (t0) cc_final: 0.8155 (t0) REVERT: D 128 SER cc_start: 0.6986 (t) cc_final: 0.6541 (m) REVERT: D 133 TYR cc_start: 0.6585 (t80) cc_final: 0.6003 (t80) REVERT: D 136 LYS cc_start: 0.8764 (tttt) cc_final: 0.8474 (mtpt) REVERT: D 143 GLU cc_start: 0.6354 (mt-10) cc_final: 0.5925 (mt-10) REVERT: E 3 ILE cc_start: 0.8820 (pt) cc_final: 0.8336 (tt) REVERT: E 132 ILE cc_start: 0.6487 (mt) cc_final: 0.5925 (mp) REVERT: F 21 ASP cc_start: 0.6480 (t0) cc_final: 0.6089 (p0) REVERT: F 110 ASP cc_start: 0.6291 (p0) cc_final: 0.6054 (t0) REVERT: F 149 LEU cc_start: 0.7376 (mt) cc_final: 0.7066 (mt) REVERT: G 235 THR cc_start: 0.7889 (m) cc_final: 0.7669 (p) REVERT: G 277 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7056 (tm-30) REVERT: G 293 TYR cc_start: 0.8516 (t80) cc_final: 0.8223 (t80) REVERT: G 336 ASP cc_start: 0.7714 (t0) cc_final: 0.7508 (t0) REVERT: G 396 LYS cc_start: 0.8058 (tttt) cc_final: 0.7802 (tptt) REVERT: G 418 ARG cc_start: 0.8455 (ptt180) cc_final: 0.8058 (ptt180) REVERT: H 93 TYR cc_start: 0.4808 (p90) cc_final: 0.4014 (p90) REVERT: H 399 GLN cc_start: 0.6650 (mm-40) cc_final: 0.6449 (mt0) REVERT: H 402 ILE cc_start: 0.8466 (pt) cc_final: 0.8266 (tp) REVERT: I 128 LEU cc_start: 0.8175 (mp) cc_final: 0.7516 (mp) REVERT: I 150 ASN cc_start: 0.6638 (p0) cc_final: 0.6212 (m-40) REVERT: I 182 MET cc_start: 0.7295 (ptp) cc_final: 0.7077 (ptp) REVERT: I 184 ARG cc_start: 0.4206 (ttp-170) cc_final: 0.3844 (tpm170) REVERT: J 70 GLU cc_start: 0.6057 (mt-10) cc_final: 0.5579 (mt-10) REVERT: J 77 ARG cc_start: 0.6137 (ttp-110) cc_final: 0.5935 (tpt90) REVERT: J 399 GLN cc_start: 0.6993 (mm-40) cc_final: 0.6723 (pt0) outliers start: 3 outliers final: 0 residues processed: 580 average time/residue: 0.1334 time to fit residues: 112.2032 Evaluate side-chains 302 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 910 ASN B 126 GLN C 38 ASN C 50 GLN C 155 GLN C 162 GLN D 84 ASN E 74 ASN G 303 ASN G 321 ASN H 62 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120410 restraints weight = 27152.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121149 restraints weight = 19248.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121651 restraints weight = 15177.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122272 restraints weight = 12117.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122682 restraints weight = 9988.972| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15000 Z= 0.142 Angle : 0.579 9.036 20340 Z= 0.308 Chirality : 0.046 0.195 2247 Planarity : 0.004 0.050 2623 Dihedral : 3.996 49.571 1997 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.89 % Allowed : 9.76 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.20), residues: 1789 helix: 0.90 (0.44), residues: 146 sheet: 0.60 (0.22), residues: 545 loop : 0.03 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 118 TYR 0.026 0.002 TYR D 133 PHE 0.017 0.002 PHE C 151 TRP 0.009 0.001 TRP C 33 HIS 0.003 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (15000) covalent geometry : angle 0.57911 / 0.31 (20340) hydrogen bonds : bond 0.05389 / 3.47 ( 463) hydrogen bonds : angle 6.58896 / 4.68 ( 1305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 347 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 850 ASP cc_start: 0.6073 (t0) cc_final: 0.5812 (t0) REVERT: A 851 ILE cc_start: 0.8699 (mt) cc_final: 0.8452 (mt) REVERT: A 884 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7031 (mm-30) REVERT: B 13 ARG cc_start: 0.7092 (mmt-90) cc_final: 0.6378 (mtm180) REVERT: C 141 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6832 (mt-10) REVERT: D 40 GLN cc_start: 0.8743 (mt0) cc_final: 0.8320 (mt0) REVERT: D 59 ASP cc_start: 0.7195 (t0) cc_final: 0.6852 (t0) REVERT: D 61 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7730 (mm-40) REVERT: D 72 ASN cc_start: 0.7308 (m-40) cc_final: 0.7041 (m110) REVERT: E 3 ILE cc_start: 0.8681 (pt) cc_final: 0.8202 (tt) REVERT: F 21 ASP cc_start: 0.6732 (t0) cc_final: 0.6131 (p0) REVERT: F 110 ASP cc_start: 0.6810 (p0) cc_final: 0.6360 (t0) REVERT: F 154 LYS cc_start: 0.8172 (mttp) cc_final: 0.7926 (mttt) REVERT: G 235 THR cc_start: 0.8082 (m) cc_final: 0.7748 (p) REVERT: G 277 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7163 (tm-30) REVERT: G 293 TYR cc_start: 0.8674 (t80) cc_final: 0.8168 (t80) REVERT: G 360 SER cc_start: 0.8898 (t) cc_final: 0.8388 (m) REVERT: G 376 TYR cc_start: 0.7951 (t80) cc_final: 0.7532 (t80) REVERT: H 86 TYR cc_start: 0.4706 (OUTLIER) cc_final: 0.3645 (p90) REVERT: H 93 TYR cc_start: 0.4932 (p90) cc_final: 0.4296 (p90) REVERT: H 133 LEU cc_start: 0.6676 (mm) cc_final: 0.6452 (mp) REVERT: I 150 ASN cc_start: 0.7183 (p0) cc_final: 0.6471 (m-40) REVERT: I 184 ARG cc_start: 0.4687 (ttp-170) cc_final: 0.4169 (tpm170) REVERT: J 132 GLU cc_start: 0.8254 (mp0) cc_final: 0.7933 (mp0) outliers start: 48 outliers final: 30 residues processed: 377 average time/residue: 0.1131 time to fit residues: 65.1733 Evaluate side-chains 306 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain J residue 97 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 60 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN I 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.128565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118918 restraints weight = 27764.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119670 restraints weight = 18864.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120452 restraints weight = 14645.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120844 restraints weight = 11404.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121487 restraints weight = 9489.712| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15000 Z= 0.134 Angle : 0.550 7.609 20340 Z= 0.293 Chirality : 0.046 0.262 2247 Planarity : 0.004 0.052 2623 Dihedral : 4.045 19.067 1995 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.67 % Allowed : 12.59 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1789 helix: 0.62 (0.43), residues: 146 sheet: 0.63 (0.23), residues: 523 loop : -0.22 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 118 TYR 0.022 0.001 TYR I 86 PHE 0.028 0.002 PHE F 156 TRP 0.013 0.001 TRP C 33 HIS 0.002 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (15000) covalent geometry : angle 0.54969 / 0.29 (20340) hydrogen bonds : bond 0.04425 / 2.88 ( 463) hydrogen bonds : angle 6.09523 / 4.33 ( 1305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 288 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 850 ASP cc_start: 0.6392 (t0) cc_final: 0.6174 (t0) REVERT: A 851 ILE cc_start: 0.8727 (mt) cc_final: 0.8469 (mt) REVERT: A 884 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7062 (mm-30) REVERT: B 13 ARG cc_start: 0.7265 (mmt-90) cc_final: 0.6734 (mtm180) REVERT: C 147 THR cc_start: 0.6403 (m) cc_final: 0.5924 (p) REVERT: D 40 GLN cc_start: 0.8408 (mt0) cc_final: 0.8202 (mt0) REVERT: D 59 ASP cc_start: 0.7152 (t0) cc_final: 0.6626 (t0) REVERT: D 61 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7677 (mm-40) REVERT: D 68 LEU cc_start: 0.8238 (tp) cc_final: 0.7864 (tt) REVERT: E 3 ILE cc_start: 0.8609 (pt) cc_final: 0.8136 (tt) REVERT: F 21 ASP cc_start: 0.6779 (t0) cc_final: 0.6113 (p0) REVERT: F 110 ASP cc_start: 0.6843 (p0) cc_final: 0.6424 (t0) REVERT: G 235 THR cc_start: 0.8137 (m) cc_final: 0.7843 (p) REVERT: G 277 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7119 (tm-30) REVERT: G 293 TYR cc_start: 0.8664 (t80) cc_final: 0.8360 (t80) REVERT: G 360 SER cc_start: 0.8880 (t) cc_final: 0.8335 (m) REVERT: G 376 TYR cc_start: 0.7838 (t80) cc_final: 0.7406 (t80) REVERT: H 86 TYR cc_start: 0.4642 (OUTLIER) cc_final: 0.3585 (p90) REVERT: H 93 TYR cc_start: 0.5162 (p90) cc_final: 0.4675 (p90) REVERT: I 184 ARG cc_start: 0.4811 (ttp-170) cc_final: 0.4039 (tpm170) outliers start: 61 outliers final: 41 residues processed: 327 average time/residue: 0.1105 time to fit residues: 56.2744 Evaluate side-chains 305 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 160 GLU Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 400 GLU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 142 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 104 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 0.0000 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN E 136 ASN F 41 GLN F 157 GLN ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN I 139 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109408 restraints weight = 28309.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110222 restraints weight = 19898.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110634 restraints weight = 15784.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111218 restraints weight = 12682.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111580 restraints weight = 10648.816| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 15000 Z= 0.284 Angle : 0.704 9.077 20340 Z= 0.375 Chirality : 0.051 0.300 2247 Planarity : 0.005 0.054 2623 Dihedral : 5.267 20.572 1995 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.22 % Allowed : 13.61 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 1789 helix: 0.11 (0.42), residues: 135 sheet: 0.19 (0.23), residues: 511 loop : -0.70 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 118 TYR 0.034 0.003 TYR I 86 PHE 0.025 0.003 PHE D 55 TRP 0.017 0.002 TRP E 33 HIS 0.003 0.001 HIS A 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.28 (15000) covalent geometry : angle 0.70437 / 0.38 (20340) hydrogen bonds : bond 0.04729 / 3.10 ( 463) hydrogen bonds : angle 6.09268 / 4.30 ( 1305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 274 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 PRO cc_start: 0.8623 (Cg_exo) cc_final: 0.8417 (Cg_endo) REVERT: A 146 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8216 (m) REVERT: B 13 ARG cc_start: 0.7704 (mmt-90) cc_final: 0.7113 (mtm180) REVERT: B 118 ASP cc_start: 0.7496 (p0) cc_final: 0.6794 (p0) REVERT: C 172 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6961 (tt0) REVERT: D 13 ARG cc_start: 0.7560 (ttm110) cc_final: 0.6889 (ttm170) REVERT: D 59 ASP cc_start: 0.7343 (t0) cc_final: 0.6849 (t0) REVERT: D 61 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8116 (mm-40) REVERT: D 68 LEU cc_start: 0.8621 (tp) cc_final: 0.8245 (tt) REVERT: D 82 TYR cc_start: 0.8339 (t80) cc_final: 0.8018 (t80) REVERT: D 162 ASP cc_start: 0.8112 (t0) cc_final: 0.7817 (m-30) REVERT: E 3 ILE cc_start: 0.8820 (pt) cc_final: 0.8325 (tt) REVERT: F 21 ASP cc_start: 0.7004 (t0) cc_final: 0.6420 (p0) REVERT: F 110 ASP cc_start: 0.7296 (p0) cc_final: 0.6660 (t0) REVERT: G 277 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7317 (tt0) REVERT: G 327 TYR cc_start: 0.8561 (t80) cc_final: 0.7691 (t80) REVERT: G 437 ASP cc_start: 0.8964 (t0) cc_final: 0.8639 (t0) REVERT: H 86 TYR cc_start: 0.4111 (OUTLIER) cc_final: 0.2984 (p90) REVERT: H 89 TYR cc_start: 0.7408 (m-80) cc_final: 0.7184 (m-80) REVERT: H 93 TYR cc_start: 0.5665 (p90) cc_final: 0.5035 (p90) REVERT: J 48 ILE cc_start: 0.6169 (mm) cc_final: 0.5961 (mt) REVERT: J 99 TYR cc_start: 0.6432 (m-80) cc_final: 0.5292 (m-80) outliers start: 70 outliers final: 55 residues processed: 327 average time/residue: 0.1131 time to fit residues: 56.9491 Evaluate side-chains 302 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 400 GLU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 183 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 124 optimal weight: 0.6980 chunk 159 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN A 61 GLN B 40 GLN F 41 GLN G 321 ASN G 414 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110925 restraints weight = 27467.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112789 restraints weight = 17454.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114173 restraints weight = 10991.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114512 restraints weight = 8201.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114818 restraints weight = 6908.178| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15000 Z= 0.124 Angle : 0.565 7.862 20340 Z= 0.301 Chirality : 0.046 0.291 2247 Planarity : 0.004 0.051 2623 Dihedral : 4.753 20.307 1995 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.86 % Allowed : 15.48 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 1789 helix: 0.65 (0.44), residues: 128 sheet: 0.14 (0.23), residues: 515 loop : -0.56 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 118 TYR 0.027 0.001 TYR E 117 PHE 0.019 0.002 PHE C 151 TRP 0.013 0.001 TRP C 33 HIS 0.002 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (15000) covalent geometry : angle 0.56473 / 0.30 (20340) hydrogen bonds : bond 0.03876 / 2.55 ( 463) hydrogen bonds : angle 5.76486 / 4.09 ( 1305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 284 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 PRO cc_start: 0.8589 (Cg_exo) cc_final: 0.8355 (Cg_endo) REVERT: A 850 ASP cc_start: 0.6576 (t0) cc_final: 0.6242 (t0) REVERT: A 851 ILE cc_start: 0.8853 (mt) cc_final: 0.8525 (mp) REVERT: B 40 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8149 (tp-100) REVERT: B 118 ASP cc_start: 0.7545 (p0) cc_final: 0.7001 (p0) REVERT: C 147 THR cc_start: 0.6542 (m) cc_final: 0.6019 (p) REVERT: C 169 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: C 172 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: D 59 ASP cc_start: 0.7340 (t0) cc_final: 0.6820 (t0) REVERT: D 68 LEU cc_start: 0.8437 (tp) cc_final: 0.8099 (tt) REVERT: D 82 TYR cc_start: 0.7940 (t80) cc_final: 0.7554 (t80) REVERT: D 162 ASP cc_start: 0.8238 (t0) cc_final: 0.7522 (m-30) REVERT: E 3 ILE cc_start: 0.8872 (pt) cc_final: 0.8353 (tt) REVERT: E 96 GLU cc_start: 0.5101 (tt0) cc_final: 0.4884 (mt-10) REVERT: E 103 LEU cc_start: 0.8603 (mp) cc_final: 0.8380 (mt) REVERT: F 21 ASP cc_start: 0.7148 (t0) cc_final: 0.6420 (p0) REVERT: F 110 ASP cc_start: 0.7164 (p0) cc_final: 0.6606 (t0) REVERT: G 277 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7316 (tt0) REVERT: G 327 TYR cc_start: 0.8441 (t80) cc_final: 0.7444 (t80) REVERT: G 360 SER cc_start: 0.8817 (t) cc_final: 0.8144 (m) REVERT: G 437 ASP cc_start: 0.8840 (t0) cc_final: 0.8466 (t0) REVERT: H 86 TYR cc_start: 0.4600 (OUTLIER) cc_final: 0.3425 (p90) REVERT: H 93 TYR cc_start: 0.5614 (p90) cc_final: 0.4978 (p90) REVERT: I 81 ARG cc_start: 0.6633 (ttt-90) cc_final: 0.6375 (ttt180) REVERT: I 184 ARG cc_start: 0.4730 (ttp-170) cc_final: 0.4181 (tpp-160) REVERT: J 99 TYR cc_start: 0.6312 (m-80) cc_final: 0.5393 (m-80) outliers start: 64 outliers final: 41 residues processed: 325 average time/residue: 0.1084 time to fit residues: 54.2555 Evaluate side-chains 304 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain G residue 231 ASP Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 183 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 chunk 145 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN D 72 ASN F 41 GLN G 374 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109193 restraints weight = 27785.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110908 restraints weight = 17816.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112253 restraints weight = 11457.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112580 restraints weight = 8647.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112661 restraints weight = 7328.257| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15000 Z= 0.177 Angle : 0.592 7.946 20340 Z= 0.316 Chirality : 0.047 0.309 2247 Planarity : 0.004 0.053 2623 Dihedral : 4.821 20.145 1995 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.22 % Allowed : 16.02 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.19), residues: 1789 helix: 0.38 (0.44), residues: 134 sheet: 0.11 (0.23), residues: 511 loop : -0.63 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 118 TYR 0.031 0.002 TYR I 86 PHE 0.019 0.002 PHE C 151 TRP 0.012 0.001 TRP C 33 HIS 0.002 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (15000) covalent geometry : angle 0.59241 / 0.32 (20340) hydrogen bonds : bond 0.03942 / 2.60 ( 463) hydrogen bonds : angle 5.73227 / 4.05 ( 1305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 257 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8492 (mttt) cc_final: 0.7543 (tttt) REVERT: A 131 PRO cc_start: 0.8595 (Cg_exo) cc_final: 0.8364 (Cg_endo) REVERT: A 850 ASP cc_start: 0.6622 (t0) cc_final: 0.6246 (t0) REVERT: A 851 ILE cc_start: 0.8876 (mt) cc_final: 0.8562 (mt) REVERT: B 13 ARG cc_start: 0.7723 (mmt-90) cc_final: 0.6913 (mtm180) REVERT: B 118 ASP cc_start: 0.7608 (p0) cc_final: 0.7084 (p0) REVERT: C 147 THR cc_start: 0.6601 (m) cc_final: 0.5995 (p) REVERT: C 169 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: C 172 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: D 59 ASP cc_start: 0.7359 (t0) cc_final: 0.6910 (t0) REVERT: D 82 TYR cc_start: 0.8001 (t80) cc_final: 0.7646 (t80) REVERT: D 161 MET cc_start: 0.6788 (tpt) cc_final: 0.6353 (tpt) REVERT: D 162 ASP cc_start: 0.7914 (t0) cc_final: 0.7429 (m-30) REVERT: E 3 ILE cc_start: 0.8859 (pt) cc_final: 0.8475 (tt) REVERT: E 96 GLU cc_start: 0.5222 (tt0) cc_final: 0.4961 (mt-10) REVERT: F 21 ASP cc_start: 0.7170 (t0) cc_final: 0.6457 (p0) REVERT: F 110 ASP cc_start: 0.7260 (p0) cc_final: 0.6699 (t0) REVERT: G 271 MET cc_start: 0.6941 (tpt) cc_final: 0.6593 (tpt) REVERT: G 277 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7532 (tt0) REVERT: G 327 TYR cc_start: 0.8519 (t80) cc_final: 0.7609 (t80) REVERT: G 360 SER cc_start: 0.8874 (t) cc_final: 0.8188 (m) REVERT: G 437 ASP cc_start: 0.8872 (t0) cc_final: 0.8479 (t0) REVERT: H 86 TYR cc_start: 0.4499 (OUTLIER) cc_final: 0.3324 (p90) REVERT: I 81 ARG cc_start: 0.6716 (ttt-90) cc_final: 0.6502 (ttt180) REVERT: I 184 ARG cc_start: 0.4479 (ttp-170) cc_final: 0.4100 (tpp-160) REVERT: J 99 TYR cc_start: 0.6408 (m-80) cc_final: 0.5384 (m-80) REVERT: J 132 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.7507 (mp0) outliers start: 70 outliers final: 56 residues processed: 304 average time/residue: 0.1035 time to fit residues: 49.0219 Evaluate side-chains 305 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 245 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain G residue 231 ASP Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 183 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 16 optimal weight: 0.0050 chunk 19 optimal weight: 4.9990 chunk 109 optimal weight: 0.0470 chunk 145 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.7896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN D 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111421 restraints weight = 27346.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112949 restraints weight = 19022.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114393 restraints weight = 12526.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114722 restraints weight = 9369.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114896 restraints weight = 7792.896| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15000 Z= 0.121 Angle : 0.557 8.399 20340 Z= 0.296 Chirality : 0.046 0.292 2247 Planarity : 0.004 0.053 2623 Dihedral : 4.609 19.848 1995 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.49 % Allowed : 17.41 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 1789 helix: 0.65 (0.45), residues: 128 sheet: 0.24 (0.23), residues: 500 loop : -0.59 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 205 TYR 0.026 0.001 TYR E 117 PHE 0.020 0.001 PHE C 151 TRP 0.012 0.001 TRP C 33 HIS 0.002 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (15000) covalent geometry : angle 0.55695 / 0.30 (20340) hydrogen bonds : bond 0.03617 / 2.37 ( 463) hydrogen bonds : angle 5.59313 / 3.96 ( 1305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 255 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8416 (mttt) cc_final: 0.7494 (tttt) REVERT: A 131 PRO cc_start: 0.8579 (Cg_exo) cc_final: 0.8356 (Cg_endo) REVERT: A 850 ASP cc_start: 0.6534 (t0) cc_final: 0.6248 (t0) REVERT: A 851 ILE cc_start: 0.8956 (mt) cc_final: 0.8662 (mt) REVERT: B 118 ASP cc_start: 0.7410 (p0) cc_final: 0.6888 (p0) REVERT: C 147 THR cc_start: 0.6531 (m) cc_final: 0.5988 (p) REVERT: C 169 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: C 172 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6401 (tt0) REVERT: D 59 ASP cc_start: 0.7374 (t0) cc_final: 0.6344 (t0) REVERT: D 61 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8035 (mm-40) REVERT: D 82 TYR cc_start: 0.8002 (t80) cc_final: 0.7595 (t80) REVERT: D 125 ASP cc_start: 0.7814 (t0) cc_final: 0.7511 (t0) REVERT: D 162 ASP cc_start: 0.7805 (t0) cc_final: 0.7348 (m-30) REVERT: E 3 ILE cc_start: 0.8878 (pt) cc_final: 0.8455 (tt) REVERT: E 96 GLU cc_start: 0.5476 (tt0) cc_final: 0.5231 (mt-10) REVERT: F 21 ASP cc_start: 0.7133 (t0) cc_final: 0.6397 (p0) REVERT: F 110 ASP cc_start: 0.6845 (p0) cc_final: 0.6566 (t0) REVERT: G 198 GLU cc_start: 0.7910 (mp0) cc_final: 0.7660 (mp0) REVERT: G 277 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7543 (tt0) REVERT: G 327 TYR cc_start: 0.8455 (t80) cc_final: 0.7554 (t80) REVERT: G 360 SER cc_start: 0.8818 (t) cc_final: 0.8148 (m) REVERT: G 437 ASP cc_start: 0.8842 (t0) cc_final: 0.8589 (t0) REVERT: H 86 TYR cc_start: 0.4544 (OUTLIER) cc_final: 0.3429 (p90) REVERT: I 103 TYR cc_start: 0.4409 (m-80) cc_final: 0.3997 (m-10) REVERT: I 184 ARG cc_start: 0.5042 (ttp-170) cc_final: 0.4742 (tpp-160) REVERT: J 70 GLU cc_start: 0.5950 (mt-10) cc_final: 0.4663 (mt-10) REVERT: J 99 TYR cc_start: 0.6338 (m-80) cc_final: 0.5342 (m-80) REVERT: J 109 TYR cc_start: 0.4081 (m-80) cc_final: 0.3560 (m-80) outliers start: 58 outliers final: 44 residues processed: 296 average time/residue: 0.1073 time to fit residues: 49.6078 Evaluate side-chains 291 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain G residue 231 ASP Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 183 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 92 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN C 50 GLN D 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109667 restraints weight = 27559.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111516 restraints weight = 17160.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113179 restraints weight = 10483.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113446 restraints weight = 7478.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113730 restraints weight = 6232.713| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15000 Z= 0.154 Angle : 0.573 8.547 20340 Z= 0.304 Chirality : 0.046 0.293 2247 Planarity : 0.004 0.056 2623 Dihedral : 4.686 19.851 1995 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.61 % Allowed : 17.95 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1789 helix: 0.81 (0.46), residues: 128 sheet: 0.22 (0.23), residues: 512 loop : -0.64 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 77 TYR 0.029 0.002 TYR E 102 PHE 0.022 0.001 PHE C 151 TRP 0.011 0.001 TRP C 33 HIS 0.002 0.001 HIS E 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (15000) covalent geometry : angle 0.57279 / 0.30 (20340) hydrogen bonds : bond 0.03716 / 2.44 ( 463) hydrogen bonds : angle 5.55791 / 3.93 ( 1305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 249 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8017 (mp) REVERT: A 56 LYS cc_start: 0.8401 (mttt) cc_final: 0.7500 (tttt) REVERT: A 131 PRO cc_start: 0.8595 (Cg_exo) cc_final: 0.8355 (Cg_endo) REVERT: A 850 ASP cc_start: 0.6571 (t0) cc_final: 0.6278 (t0) REVERT: A 851 ILE cc_start: 0.8979 (mt) cc_final: 0.8687 (mt) REVERT: B 13 ARG cc_start: 0.7726 (mmt-90) cc_final: 0.6943 (mtm180) REVERT: B 118 ASP cc_start: 0.7474 (p0) cc_final: 0.6960 (p0) REVERT: C 29 LYS cc_start: 0.8320 (tppt) cc_final: 0.8056 (tppt) REVERT: C 147 THR cc_start: 0.6504 (m) cc_final: 0.5908 (p) REVERT: C 169 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: C 172 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6441 (tt0) REVERT: D 59 ASP cc_start: 0.7422 (t0) cc_final: 0.7106 (t0) REVERT: D 73 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8264 (t) REVERT: D 125 ASP cc_start: 0.7799 (t0) cc_final: 0.7533 (t0) REVERT: E 3 ILE cc_start: 0.8888 (pt) cc_final: 0.8460 (tt) REVERT: F 21 ASP cc_start: 0.7176 (t0) cc_final: 0.6453 (p0) REVERT: F 110 ASP cc_start: 0.6947 (p0) cc_final: 0.6658 (t0) REVERT: G 231 ASP cc_start: 0.4490 (OUTLIER) cc_final: 0.3864 (t0) REVERT: G 277 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7509 (tm-30) REVERT: G 327 TYR cc_start: 0.8514 (t80) cc_final: 0.7712 (t80) REVERT: G 437 ASP cc_start: 0.8865 (t0) cc_final: 0.8639 (t0) REVERT: H 86 TYR cc_start: 0.4434 (OUTLIER) cc_final: 0.3303 (p90) REVERT: I 81 ARG cc_start: 0.6763 (ttt180) cc_final: 0.5854 (tpt170) REVERT: I 124 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7688 (tm-30) REVERT: I 184 ARG cc_start: 0.4469 (ttp-170) cc_final: 0.4063 (tpp-160) REVERT: J 70 GLU cc_start: 0.6005 (mt-10) cc_final: 0.4744 (mt-10) REVERT: J 99 TYR cc_start: 0.6358 (m-80) cc_final: 0.5348 (m-80) REVERT: J 109 TYR cc_start: 0.3993 (m-80) cc_final: 0.3521 (m-80) REVERT: J 132 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.7505 (mp0) outliers start: 60 outliers final: 48 residues processed: 290 average time/residue: 0.1050 time to fit residues: 47.2994 Evaluate side-chains 295 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain G residue 231 ASP Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 183 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 51 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN D 72 ASN E 92 ASN F 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111747 restraints weight = 27560.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113570 restraints weight = 17138.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115342 restraints weight = 10467.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115617 restraints weight = 7430.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115635 restraints weight = 6076.702| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15000 Z= 0.111 Angle : 0.560 9.971 20340 Z= 0.295 Chirality : 0.045 0.259 2247 Planarity : 0.004 0.056 2623 Dihedral : 4.501 19.561 1995 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.31 % Allowed : 18.43 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.19), residues: 1789 helix: 1.09 (0.48), residues: 122 sheet: 0.33 (0.23), residues: 511 loop : -0.62 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 77 TYR 0.033 0.001 TYR D 82 PHE 0.021 0.001 PHE C 151 TRP 0.012 0.001 TRP C 33 HIS 0.001 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (15000) covalent geometry : angle 0.56022 / 0.29 (20340) hydrogen bonds : bond 0.03430 / 2.25 ( 463) hydrogen bonds : angle 5.42149 / 3.83 ( 1305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 256 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8081 (mp) REVERT: A 56 LYS cc_start: 0.8315 (mttt) cc_final: 0.7397 (tttt) REVERT: A 131 PRO cc_start: 0.8573 (Cg_exo) cc_final: 0.8330 (Cg_endo) REVERT: A 850 ASP cc_start: 0.6510 (t0) cc_final: 0.6229 (t0) REVERT: A 851 ILE cc_start: 0.8952 (mt) cc_final: 0.8658 (mt) REVERT: B 118 ASP cc_start: 0.7410 (p0) cc_final: 0.6937 (p0) REVERT: C 147 THR cc_start: 0.6501 (m) cc_final: 0.5931 (p) REVERT: C 169 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: C 172 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6413 (tt0) REVERT: D 59 ASP cc_start: 0.7452 (t0) cc_final: 0.6376 (t0) REVERT: D 61 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8035 (mm-40) REVERT: D 73 VAL cc_start: 0.8460 (t) cc_final: 0.8209 (t) REVERT: D 82 TYR cc_start: 0.7794 (t80) cc_final: 0.7297 (t80) REVERT: D 125 ASP cc_start: 0.7817 (t0) cc_final: 0.7477 (t0) REVERT: E 3 ILE cc_start: 0.8894 (pt) cc_final: 0.8458 (tt) REVERT: F 21 ASP cc_start: 0.7160 (t0) cc_final: 0.6436 (p0) REVERT: G 231 ASP cc_start: 0.4127 (OUTLIER) cc_final: 0.3344 (t0) REVERT: G 277 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7470 (tm-30) REVERT: G 327 TYR cc_start: 0.8462 (t80) cc_final: 0.7611 (t80) REVERT: G 360 SER cc_start: 0.8762 (t) cc_final: 0.8135 (m) REVERT: G 437 ASP cc_start: 0.8831 (t0) cc_final: 0.8562 (t0) REVERT: H 86 TYR cc_start: 0.4488 (OUTLIER) cc_final: 0.3379 (p90) REVERT: H 89 TYR cc_start: 0.7260 (m-80) cc_final: 0.7053 (m-80) REVERT: H 165 VAL cc_start: 0.7703 (t) cc_final: 0.7469 (t) REVERT: I 81 ARG cc_start: 0.6710 (ttt180) cc_final: 0.5811 (tpt170) REVERT: I 124 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7805 (tm-30) REVERT: I 184 ARG cc_start: 0.5007 (ttp-170) cc_final: 0.4710 (tpp-160) REVERT: J 109 TYR cc_start: 0.4028 (m-80) cc_final: 0.3504 (m-80) REVERT: J 132 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.7417 (mp0) outliers start: 55 outliers final: 46 residues processed: 296 average time/residue: 0.0985 time to fit residues: 45.1519 Evaluate side-chains 297 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 245 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain G residue 231 ASP Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 132 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 11 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN D 72 ASN F 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109649 restraints weight = 27819.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111431 restraints weight = 17620.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113055 restraints weight = 11175.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113428 restraints weight = 7813.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113441 restraints weight = 6438.310| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15000 Z= 0.170 Angle : 0.602 9.063 20340 Z= 0.319 Chirality : 0.047 0.250 2247 Planarity : 0.004 0.058 2623 Dihedral : 4.650 19.701 1995 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.43 % Allowed : 18.37 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1789 helix: 0.91 (0.46), residues: 128 sheet: 0.22 (0.23), residues: 517 loop : -0.67 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 205 TYR 0.031 0.002 TYR D 82 PHE 0.023 0.002 PHE C 151 TRP 0.012 0.001 TRP E 33 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (15000) covalent geometry : angle 0.60152 / 0.32 (20340) hydrogen bonds : bond 0.03667 / 2.41 ( 463) hydrogen bonds : angle 5.48646 / 3.86 ( 1305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 244 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8062 (mp) REVERT: A 44 GLN cc_start: 0.8002 (mt0) cc_final: 0.7502 (mm-40) REVERT: A 56 LYS cc_start: 0.8451 (mttt) cc_final: 0.7451 (tttt) REVERT: A 131 PRO cc_start: 0.8593 (Cg_exo) cc_final: 0.8348 (Cg_endo) REVERT: B 13 ARG cc_start: 0.7731 (mmt-90) cc_final: 0.6948 (mtm180) REVERT: B 118 ASP cc_start: 0.7629 (p0) cc_final: 0.7149 (p0) REVERT: C 29 LYS cc_start: 0.8168 (tppt) cc_final: 0.7835 (tppt) REVERT: C 147 THR cc_start: 0.6548 (m) cc_final: 0.5945 (p) REVERT: C 169 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: D 59 ASP cc_start: 0.7461 (t0) cc_final: 0.7107 (t0) REVERT: D 73 VAL cc_start: 0.8533 (t) cc_final: 0.8308 (t) REVERT: D 82 TYR cc_start: 0.7918 (t80) cc_final: 0.7473 (t80) REVERT: D 125 ASP cc_start: 0.7797 (t0) cc_final: 0.7504 (t0) REVERT: E 3 ILE cc_start: 0.8873 (pt) cc_final: 0.8435 (tt) REVERT: F 21 ASP cc_start: 0.7176 (t0) cc_final: 0.6453 (p0) REVERT: G 231 ASP cc_start: 0.4333 (OUTLIER) cc_final: 0.3559 (t0) REVERT: G 277 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7486 (tm-30) REVERT: G 327 TYR cc_start: 0.8491 (t80) cc_final: 0.7626 (t80) REVERT: G 360 SER cc_start: 0.8814 (t) cc_final: 0.8161 (m) REVERT: H 86 TYR cc_start: 0.4521 (OUTLIER) cc_final: 0.3357 (p90) REVERT: H 165 VAL cc_start: 0.7828 (t) cc_final: 0.7602 (t) REVERT: I 81 ARG cc_start: 0.6786 (ttt180) cc_final: 0.5854 (tpt170) REVERT: I 124 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7809 (tm-30) REVERT: I 184 ARG cc_start: 0.4506 (ttp-170) cc_final: 0.4206 (tpp-160) REVERT: J 132 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.7499 (mp0) outliers start: 57 outliers final: 47 residues processed: 286 average time/residue: 0.0957 time to fit residues: 42.6406 Evaluate side-chains 292 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 240 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain G residue 231 ASP Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 182 MET Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 132 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 139 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 170 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN D 72 ASN F 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.122733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110934 restraints weight = 27389.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112784 restraints weight = 17040.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114466 restraints weight = 10453.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114732 restraints weight = 7550.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114853 restraints weight = 6215.667| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15000 Z= 0.125 Angle : 0.581 9.164 20340 Z= 0.307 Chirality : 0.046 0.237 2247 Planarity : 0.004 0.056 2623 Dihedral : 4.562 19.537 1995 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.25 % Allowed : 18.92 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 1789 helix: 1.07 (0.48), residues: 122 sheet: 0.29 (0.23), residues: 511 loop : -0.68 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 205 TYR 0.032 0.001 TYR E 102 PHE 0.022 0.001 PHE C 151 TRP 0.011 0.001 TRP C 33 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (15000) covalent geometry : angle 0.58058 / 0.31 (20340) hydrogen bonds : bond 0.03485 / 2.28 ( 463) hydrogen bonds : angle 5.43637 / 3.83 ( 1305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2319.27 seconds wall clock time: 41 minutes 5.83 seconds (2465.83 seconds total)