Starting phenix.real_space_refine on Thu Aug 6 16:32:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tio_55963/08_2026/9tio_55963.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tio_55963/08_2026/9tio_55963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tio_55963/08_2026/9tio_55963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tio_55963/08_2026/9tio_55963.map" model { file = "/net/cci-nas-00/data/ceres_data/9tio_55963/08_2026/9tio_55963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tio_55963/08_2026/9tio_55963.cif" } resolution = 3.9 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 31 5.16 5 C 10056 2.51 5 N 2568 2.21 5 O 3173 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s 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: 15828 Number of models: 1 Model: "" Number of chains: 11 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: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1306 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain: "C" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 889 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain breaks: 4 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: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1277 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain breaks: 1 Chain: "G" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2138 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 6, 'TRANS': 250} Chain breaks: 2 Chain: "H" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1193 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 3 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: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1209 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 2 Chain: "K" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1199 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain breaks: 2 Time building chain proxies: 3.71, per 1000 atoms: 0.23 Number of scatterers: 15828 At special positions: 0 Unit cell: (141.712, 133.376, 140.045, 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 31 16.00 O 3173 8.00 N 2568 7.00 C 10056 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: 1.14 Conformation dependent library (CDL) restraints added in 751.8 milliseconds 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3722 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 31 sheets defined 12.5% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 32 through 53 removed outlier: 3.772A pdb=" N LEU A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.579A pdb=" N LEU A 123 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'B' and resid 15 through 18 Processing helix chain 'B' and resid 32 through 53 removed outlier: 3.790A pdb=" N LEU B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'D' and resid 15 through 18 Processing helix chain 'D' and resid 32 through 53 removed outlier: 3.707A pdb=" N LEU D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'E' and resid 5 through 19 removed outlier: 3.864A pdb=" N HIS E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 10 " --> pdb=" O TYR E 6 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 19 " --> pdb=" O TYR E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 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: 3.636A pdb=" N HIS F 9 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.571A 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 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' 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 276 through 282 removed outlier: 4.278A pdb=" N ALA G 280 " --> pdb=" O ASN G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 297 removed outlier: 4.158A pdb=" N TYR G 294 " --> pdb=" O PRO G 290 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR G 297 " --> pdb=" O TYR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 332 Processing helix chain 'G' and resid 341 through 351 Processing helix chain 'H' and resid 47 through 51 Processing helix chain 'I' and resid 44 through 51 removed outlier: 3.621A pdb=" N ILE I 48 " --> pdb=" O PHE I 45 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU I 49 " --> pdb=" O ASN I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 133 Processing helix chain 'J' and resid 44 through 46 No H-bonds generated for 'chain 'J' and resid 44 through 46' Processing helix chain 'J' and resid 47 through 52 removed outlier: 3.901A pdb=" N SER J 51 " --> pdb=" O ASN J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 133 removed outlier: 3.571A pdb=" N LEU J 133 " --> pdb=" O VAL J 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 18 removed outlier: 4.288A pdb=" N HIS K 9 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL K 10 " --> pdb=" O TYR K 6 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU K 11 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU K 12 " --> pdb=" O SER K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 97 removed outlier: 3.953A pdb=" N LYS K 94 " --> pdb=" O PRO K 90 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA K 95 " --> pdb=" O GLU K 91 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY K 97 " --> pdb=" O ALA K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 140 No H-bonds generated for 'chain 'K' and resid 138 through 140' Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 24 removed outlier: 6.402A pdb=" N ARG A 20 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU B 143 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 22 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU B 104 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR B 159 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 106 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 155 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR B 159 " --> pdb=" O TYR B 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.433A pdb=" N TYR A 80 " --> pdb=" O GLN A 61 " (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: 6.694A pdb=" N ILE A 106 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N THR A 159 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU A 104 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS D 22 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU A 143 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 5.876A 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: 3.513A pdb=" N THR A 571 " --> pdb=" O ILE A 938 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE A 938 " --> pdb=" O THR A 571 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR A 573 " --> pdb=" O PHE A 936 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N PHE A 936 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 808 " --> pdb=" O TYR A 939 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N THR A 805 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 11.593A pdb=" N ASP A 867 " --> pdb=" O THR A 805 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER A 807 " --> pdb=" O PHE A 865 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 865 " --> pdb=" O SER A 807 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 582 removed outlier: 6.148A 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: 5.469A pdb=" N GLY A 829 " --> pdb=" O ASN A 837 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR A 839 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 827 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N TYR A 841 " --> pdb=" O ILE A 825 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N ILE A 825 " --> pdb=" O TYR A 841 " (cutoff:3.500A) removed outlier: 9.817A pdb=" N GLU A 843 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 11.248A pdb=" N VAL A 823 " --> pdb=" O GLU A 843 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 917 " --> pdb=" O HIS A 929 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 20 through 24 removed outlier: 5.679A pdb=" N ARG B 20 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU D 143 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS B 22 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU D 104 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR D 159 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE D 106 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.275A pdb=" N LYS B 60 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR B 82 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 62 " --> pdb=" O TYR B 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AB3, first strand: chain 'C' and resid 52 through 57 removed outlier: 3.693A pdb=" N GLY C 54 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ARG C 118 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN C 153 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL C 120 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE C 151 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE C 122 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 78 through 80 removed outlier: 6.463A pdb=" N THR F 164 " --> pdb=" O PHE G 203 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ARG G 205 " --> pdb=" O THR F 164 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS F 166 " --> pdb=" O ARG G 205 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR G 207 " --> pdb=" O LYS F 166 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG F 168 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS F 60 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F 63 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N SER F 84 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS F 83 " --> pdb=" O TYR F 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.290A pdb=" N LYS D 60 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N TYR D 82 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY D 79 " --> pdb=" O TYR D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 73 through 75 Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.693A pdb=" N ILE E 3 " --> pdb=" O PHE F 151 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE F 151 " --> pdb=" O ILE E 3 " (cutoff:3.500A) removed outlier: 10.051A pdb=" N PHE F 151 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N VAL F 123 " --> pdb=" O PHE F 151 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N ASN F 153 " --> pdb=" O GLY F 121 " (cutoff:3.500A) removed outlier: 9.881A pdb=" N GLY F 121 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N GLN F 155 " --> pdb=" O GLN F 119 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN F 119 " --> pdb=" O GLN F 155 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY F 115 " --> pdb=" O ARG F 159 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY F 54 " --> pdb=" O ILE F 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 136 through 137 removed outlier: 8.419A pdb=" N ARG E 118 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN E 153 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL E 120 " --> pdb=" O PHE E 151 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE E 151 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE E 122 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 151 " --> pdb=" O ILE F 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE F 3 " --> pdb=" O PHE E 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 78 through 80 removed outlier: 3.837A pdb=" N LEU E 63 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER G 464 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG E 168 " --> pdb=" O TYR G 460 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N THR K 164 " --> pdb=" O ASN G 459 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU G 461 " --> pdb=" O THR K 164 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS K 166 " --> pdb=" O LEU G 461 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE G 463 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG K 168 " --> pdb=" O ILE G 463 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ARG G 465 " --> pdb=" O ARG K 168 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE K 170 " --> pdb=" O ARG G 465 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR G 467 " --> pdb=" O ILE K 170 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL K 171 " --> pdb=" O VAL K 101 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL K 101 " --> pdb=" O VAL K 171 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP K 100 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR K 62 " --> pdb=" O TYR K 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.828A pdb=" N VAL E 127 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AC3, first strand: chain 'G' and resid 213 through 218 Processing sheet with id=AC4, first strand: chain 'G' and resid 213 through 218 removed outlier: 5.342A pdb=" N VAL G 433 " --> pdb=" O SER G 360 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N SER G 360 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR G 435 " --> pdb=" O TYR G 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 287 through 288 removed outlier: 3.524A pdb=" N SER G 316 " --> pdb=" O ILE G 421 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N PHE G 416 " --> pdb=" O TYR G 376 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU G 370 " --> pdb=" O ASN G 422 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE G 369 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN G 390 " --> pdb=" O ILE G 369 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE G 371 " --> pdb=" O ILE G 388 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE G 388 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU G 373 " --> pdb=" O VAL G 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 38 through 39 removed outlier: 6.467A pdb=" N LYS H 38 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER H 113 " --> pdb=" O ASP J 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 124 through 128 removed outlier: 4.703A pdb=" N GLU H 124 " --> pdb=" O TYR H 140 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR H 142 " --> pdb=" O GLU H 124 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASN H 126 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA H 141 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY H 154 " --> pdb=" O ALA H 141 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP H 155 " --> pdb=" O ASN H 172 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 39 through 41 removed outlier: 3.774A pdb=" N THR I 61 " --> pdb=" O ILE I 40 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR I 85 " --> pdb=" O ARG I 81 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR I 86 " --> pdb=" O TYR I 103 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N THR I 102 " --> pdb=" O ASP I 110 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASP I 110 " --> pdb=" O THR I 102 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA I 104 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 124 through 128 removed outlier: 7.427A pdb=" N GLU I 124 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR I 140 " --> pdb=" O GLU I 124 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN I 126 " --> pdb=" O TYR I 140 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY I 154 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL I 169 " --> pdb=" O MET I 182 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N SER I 178 " --> pdb=" O PRO I 173 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 40 through 41 removed outlier: 3.838A pdb=" N THR J 61 " --> pdb=" O ILE J 40 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR J 86 " --> pdb=" O TYR J 103 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE J 100 " --> pdb=" O TRP J 111 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP J 111 " --> pdb=" O ILE J 100 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR J 102 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 124 through 128 removed outlier: 4.727A pdb=" N GLU J 124 " --> pdb=" O TYR J 140 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR J 142 " --> pdb=" O GLU J 124 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN J 126 " --> pdb=" O THR J 142 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY J 154 " --> pdb=" O ALA J 141 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 136 through 137 removed outlier: 3.810A pdb=" N GLY K 54 " --> pdb=" O ILE K 27 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE K 27 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR K 116 " --> pdb=" O PHE K 156 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N PHE K 156 " --> pdb=" O THR K 116 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ARG K 118 " --> pdb=" O LYS K 154 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 127 through 128 removed outlier: 4.188A pdb=" N VAL K 127 " --> pdb=" O SER K 144 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1368 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: 3.25 Time building geometry restraints manager: 1.61 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: 5067 1.34 - 1.46: 3177 1.46 - 1.57: 7849 1.57 - 1.69: 0 1.69 - 1.80: 62 Bond restraints: 16155 Sorted by residual: bond pdb=" C SER K 30 " pdb=" N THR K 31 " ideal model delta sigma weight residual 1.330 1.352 -0.022 1.47e-02 4.63e+03 2.23e+00 bond pdb=" CA GLN I 42 " pdb=" CB GLN I 42 " ideal model delta sigma weight residual 1.522 1.531 -0.009 7.00e-03 2.04e+04 1.56e+00 bond pdb=" C GLY A 834 " pdb=" N TYR A 835 " ideal model delta sigma weight residual 1.327 1.347 -0.020 1.71e-02 3.42e+03 1.36e+00 bond pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.10e+00 bond pdb=" CA VAL D 73 " pdb=" CB VAL D 73 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.03e+00 ... (remaining 16150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 20585 0.90 - 1.79: 1088 1.79 - 2.69: 133 2.69 - 3.58: 84 3.58 - 4.48: 13 Bond angle restraints: 21903 Sorted by residual: angle pdb=" N ILE B 54 " pdb=" CA ILE B 54 " pdb=" C ILE B 54 " ideal model delta sigma weight residual 111.62 109.32 2.30 7.90e-01 1.60e+00 8.46e+00 angle pdb=" N SER E 22 " pdb=" CA SER E 22 " pdb=" C SER E 22 " ideal model delta sigma weight residual 107.23 111.71 -4.48 1.67e+00 3.59e-01 7.19e+00 angle pdb=" N ASN J 150 " pdb=" CA ASN J 150 " pdb=" CB ASN J 150 " ideal model delta sigma weight residual 114.17 111.12 3.05 1.14e+00 7.69e-01 7.17e+00 angle pdb=" N ILE D 54 " pdb=" CA ILE D 54 " pdb=" C ILE D 54 " ideal model delta sigma weight residual 111.62 109.52 2.10 7.90e-01 1.60e+00 7.07e+00 angle pdb=" N ILE G 405 " pdb=" CA ILE G 405 " pdb=" C ILE G 405 " ideal model delta sigma weight residual 111.91 109.60 2.31 8.90e-01 1.26e+00 6.73e+00 ... (remaining 21898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 9473 17.31 - 34.62: 165 34.62 - 51.93: 37 51.93 - 69.23: 4 69.23 - 86.54: 5 Dihedral angle restraints: 9684 sinusoidal: 3874 harmonic: 5810 Sorted by residual: dihedral pdb=" N TYR H 103 " pdb=" CA TYR H 103 " pdb=" CB TYR H 103 " pdb=" CG TYR H 103 " ideal model delta sinusoidal sigma weight residual -60.00 -117.10 57.10 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N TYR G 468 " pdb=" CA TYR G 468 " pdb=" CB TYR G 468 " pdb=" CG TYR G 468 " ideal model delta sinusoidal sigma weight residual 180.00 -129.94 -50.06 3 1.50e+01 4.44e-03 8.85e+00 dihedral pdb=" N TRP K 85 " pdb=" CA TRP K 85 " pdb=" CB TRP K 85 " pdb=" CG TRP K 85 " ideal model delta sinusoidal sigma weight residual -60.00 -109.72 49.72 3 1.50e+01 4.44e-03 8.81e+00 ... (remaining 9681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1528 0.029 - 0.058: 590 0.058 - 0.087: 80 0.087 - 0.116: 182 0.116 - 0.145: 39 Chirality restraints: 2419 Sorted by residual: chirality pdb=" CA ILE A 588 " pdb=" N ILE A 588 " pdb=" C ILE A 588 " pdb=" CB ILE A 588 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 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 2.58 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA VAL K 138 " pdb=" N VAL K 138 " pdb=" C VAL K 138 " pdb=" CB VAL K 138 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 2416 not shown) Planarity restraints: 2819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 116 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO D 117 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 117 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 117 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 130 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 131 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL K 138 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO K 139 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO K 139 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO K 139 " -0.016 5.00e-02 4.00e+02 ... (remaining 2816 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 199 2.62 - 3.19: 13954 3.19 - 3.76: 22275 3.76 - 4.33: 33279 4.33 - 4.90: 56396 Nonbonded interactions: 126103 Sorted by model distance: nonbonded pdb=" OH TYR I 85 " pdb=" OD1 ASN I 105 " model vdw 2.046 3.040 nonbonded pdb=" OG SER B 69 " pdb=" OD1 ASP B 71 " model vdw 2.053 3.040 nonbonded pdb=" OD1 ASN A 922 " pdb=" OG SER A 924 " model vdw 2.093 3.040 nonbonded pdb=" OG1 THR D 99 " pdb=" OE2 GLU D 104 " model vdw 2.107 3.040 nonbonded pdb=" O LEU G 246 " pdb=" OG1 THR G 247 " model vdw 2.154 3.040 ... (remaining 126098 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' selection = (chain 'D' and resid 4 through 168) } ncs_group { reference = (chain 'E' and (resid 4 through 42 or resid 49 through 66 or resid 78 through 17 \ 2)) selection = (chain 'F' and (resid 4 through 42 or resid 49 through 66 or resid 78 through 17 \ 2)) selection = chain 'K' } ncs_group { reference = (chain 'H' and (resid 39 through 92 or resid 96 through 404)) selection = (chain 'I' and (resid 39 through 64 or resid 75 through 92 or resid 96 through 1 \ 03 or resid 109 through 404)) selection = (chain 'J' and (resid 39 through 64 or resid 75 through 103 or resid 109 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: 0.390 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: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.940 Find NCS groups from input model: 0.240 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 0.022 16155 Z= 0.109 Angle : 0.481 4.478 21903 Z= 0.299 Chirality : 0.042 0.145 2419 Planarity : 0.003 0.032 2819 Dihedral : 7.737 86.543 5962 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.22 % Allowed : 1.74 % Favored : 98.04 % 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: 0.89 (0.20), residues: 1925 helix: 1.60 (0.47), residues: 151 sheet: 1.34 (0.22), residues: 566 loop : 0.15 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 88 TYR 0.009 0.001 TYR D 10 PHE 0.004 0.000 PHE B 134 TRP 0.005 0.000 TRP E 33 HIS 0.001 0.000 HIS K 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.11 (16155) covalent geometry : angle 0.48102 / 0.30 (21903) hydrogen bonds : bond 0.25259 / 16.42 ( 525) hydrogen bonds : angle 8.82169 / 6.18 ( 1368) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 531 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 850 ASP cc_start: 0.6890 (t0) cc_final: 0.6591 (t0) REVERT: A 851 ILE cc_start: 0.8393 (mt) cc_final: 0.8143 (mt) REVERT: A 890 MET cc_start: 0.7984 (mtp) cc_final: 0.7618 (mtp) REVERT: B 83 ILE cc_start: 0.8954 (mt) cc_final: 0.8735 (mm) REVERT: B 145 MET cc_start: 0.7234 (mtm) cc_final: 0.6976 (mtp) REVERT: B 162 ASP cc_start: 0.7915 (m-30) cc_final: 0.7693 (m-30) REVERT: C 27 ILE cc_start: 0.8782 (mt) cc_final: 0.8438 (mt) REVERT: C 83 LYS cc_start: 0.7375 (mttt) cc_final: 0.6947 (mttt) REVERT: C 85 TRP cc_start: 0.6756 (m100) cc_final: 0.6525 (m100) REVERT: C 148 LEU cc_start: 0.7499 (tp) cc_final: 0.7000 (pp) REVERT: C 156 PHE cc_start: 0.7310 (p90) cc_final: 0.6923 (p90) REVERT: D 24 LEU cc_start: 0.8904 (mt) cc_final: 0.8231 (mp) REVERT: D 75 THR cc_start: 0.9117 (m) cc_final: 0.8516 (p) REVERT: D 90 TYR cc_start: 0.7970 (t80) cc_final: 0.7515 (t80) REVERT: D 116 THR cc_start: 0.8804 (m) cc_final: 0.8598 (p) REVERT: D 145 MET cc_start: 0.8332 (mtm) cc_final: 0.7613 (mtp) REVERT: F 53 ILE cc_start: 0.8636 (mt) cc_final: 0.8238 (tt) REVERT: F 138 VAL cc_start: 0.9026 (m) cc_final: 0.8582 (m) REVERT: F 167 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7084 (mm-30) REVERT: G 295 MET cc_start: 0.8062 (mtp) cc_final: 0.7814 (ttm) REVERT: G 304 THR cc_start: 0.8787 (m) cc_final: 0.8574 (p) REVERT: G 359 LEU cc_start: 0.9112 (mt) cc_final: 0.8753 (mt) REVERT: G 372 LYS cc_start: 0.8794 (mttt) cc_final: 0.8493 (mttm) REVERT: G 425 LYS cc_start: 0.8408 (mttp) cc_final: 0.8139 (mtpt) REVERT: H 94 SER cc_start: 0.7946 (p) cc_final: 0.7597 (t) REVERT: I 49 LEU cc_start: 0.8516 (mt) cc_final: 0.8132 (mt) REVERT: I 128 LEU cc_start: 0.8305 (mp) cc_final: 0.8084 (mt) REVERT: I 151 LEU cc_start: 0.8094 (pp) cc_final: 0.7446 (pp) REVERT: I 170 GLU cc_start: 0.7735 (tt0) cc_final: 0.7487 (tt0) REVERT: I 184 ARG cc_start: 0.6144 (ttp-170) cc_final: 0.5386 (tmt170) REVERT: J 40 ILE cc_start: 0.8728 (mp) cc_final: 0.8484 (mm) REVERT: J 115 LYS cc_start: 0.7824 (tttp) cc_final: 0.7434 (ttmt) REVERT: J 131 LYS cc_start: 0.8108 (mttt) cc_final: 0.7458 (mmtt) REVERT: J 162 LYS cc_start: 0.7116 (tttp) cc_final: 0.6792 (ttpt) REVERT: J 404 LYS cc_start: 0.6769 (mtmt) cc_final: 0.4706 (tptt) REVERT: K 82 ASN cc_start: 0.6855 (p0) cc_final: 0.6472 (p0) REVERT: K 126 LEU cc_start: 0.7749 (tt) cc_final: 0.7441 (tp) REVERT: K 139 PRO cc_start: 0.8462 (Cg_exo) cc_final: 0.8260 (Cg_endo) outliers start: 4 outliers final: 1 residues processed: 534 average time/residue: 0.1419 time to fit residues: 110.2532 Evaluate side-chains 317 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 103 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN B 40 GLN B 44 GLN B 77 ASN B 84 ASN C 82 ASN C 119 GLN C 157 GLN D 32 GLN D 61 GLN D 84 ASN E 157 GLN F 82 ASN ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS G 321 ASN H 42 GLN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN J 397 ASN K 92 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103145 restraints weight = 29423.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103274 restraints weight = 24911.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103748 restraints weight = 23137.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.103890 restraints weight = 19310.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104194 restraints weight = 17374.300| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16155 Z= 0.160 Angle : 0.594 7.255 21903 Z= 0.321 Chirality : 0.047 0.193 2419 Planarity : 0.004 0.044 2819 Dihedral : 4.199 55.838 2149 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.58 % Allowed : 10.21 % Favored : 87.21 % 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: 0.58 (0.19), residues: 1925 helix: 0.84 (0.42), residues: 155 sheet: 1.25 (0.22), residues: 566 loop : -0.07 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 118 TYR 0.024 0.002 TYR J 58 PHE 0.015 0.002 PHE K 169 TRP 0.014 0.001 TRP K 33 HIS 0.009 0.002 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (16155) covalent geometry : angle 0.59427 / 0.32 (21903) hydrogen bonds : bond 0.05464 / 3.59 ( 525) hydrogen bonds : angle 6.51793 / 4.47 ( 1368) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 338 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8375 (mt0) cc_final: 0.8050 (mt0) REVERT: A 802 GLU cc_start: 0.7588 (pt0) cc_final: 0.7310 (pt0) REVERT: A 869 MET cc_start: 0.8371 (tmm) cc_final: 0.8009 (tmm) REVERT: A 890 MET cc_start: 0.7993 (mtp) cc_final: 0.7730 (mtp) REVERT: C 27 ILE cc_start: 0.8320 (mt) cc_final: 0.8027 (mt) REVERT: C 62 THR cc_start: 0.8707 (t) cc_final: 0.8199 (m) REVERT: C 83 LYS cc_start: 0.7043 (mttt) cc_final: 0.6637 (mttt) REVERT: C 85 TRP cc_start: 0.6882 (m100) cc_final: 0.6672 (m100) REVERT: C 148 LEU cc_start: 0.7390 (tp) cc_final: 0.6863 (pp) REVERT: D 39 MET cc_start: 0.8519 (ttp) cc_final: 0.7701 (ttp) REVERT: D 56 LYS cc_start: 0.7995 (mptt) cc_final: 0.7753 (ttpp) REVERT: D 75 THR cc_start: 0.9090 (m) cc_final: 0.8808 (p) REVERT: D 84 ASN cc_start: 0.8525 (t0) cc_final: 0.8317 (t0) REVERT: F 53 ILE cc_start: 0.8909 (mt) cc_final: 0.8406 (tt) REVERT: F 124 MET cc_start: 0.8307 (ptp) cc_final: 0.7948 (ptp) REVERT: F 167 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7030 (mm-30) REVERT: G 239 LEU cc_start: 0.7604 (mt) cc_final: 0.7328 (mp) REVERT: G 272 THR cc_start: 0.8774 (p) cc_final: 0.8378 (t) REVERT: G 304 THR cc_start: 0.8913 (m) cc_final: 0.8580 (p) REVERT: G 359 LEU cc_start: 0.9017 (mt) cc_final: 0.8621 (mt) REVERT: G 360 SER cc_start: 0.9159 (t) cc_final: 0.8921 (m) REVERT: G 375 VAL cc_start: 0.9123 (p) cc_final: 0.8862 (m) REVERT: G 406 LYS cc_start: 0.7967 (tttt) cc_final: 0.7267 (ttpt) REVERT: G 431 ILE cc_start: 0.9186 (tp) cc_final: 0.8807 (tt) REVERT: G 468 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.5246 (t80) REVERT: H 94 SER cc_start: 0.7921 (p) cc_final: 0.7555 (t) REVERT: H 103 TYR cc_start: 0.4403 (OUTLIER) cc_final: 0.4157 (m-80) REVERT: I 49 LEU cc_start: 0.8238 (mt) cc_final: 0.7620 (mt) REVERT: I 82 ASN cc_start: 0.8875 (p0) cc_final: 0.8609 (p0) REVERT: I 118 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6442 (tt0) REVERT: I 151 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7854 (pt) REVERT: I 184 ARG cc_start: 0.6893 (ttp-170) cc_final: 0.5451 (tmt170) REVERT: J 40 ILE cc_start: 0.8526 (mp) cc_final: 0.8095 (mm) REVERT: J 134 THR cc_start: 0.7995 (m) cc_final: 0.7767 (m) REVERT: K 60 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7440 (ttmm) REVERT: K 126 LEU cc_start: 0.7741 (tt) cc_final: 0.7521 (tp) outliers start: 46 outliers final: 24 residues processed: 363 average time/residue: 0.1107 time to fit residues: 63.6306 Evaluate side-chains 305 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 468 TYR Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain J residue 98 MET Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 83 optimal weight: 0.9980 chunk 122 optimal weight: 0.3980 chunk 134 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 ASN D 61 GLN F 9 HIS F 155 GLN ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103018 restraints weight = 29558.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103150 restraints weight = 25227.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.103973 restraints weight = 20781.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104178 restraints weight = 17981.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.104427 restraints weight = 16218.463| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16155 Z= 0.118 Angle : 0.531 7.398 21903 Z= 0.286 Chirality : 0.045 0.196 2419 Planarity : 0.004 0.050 2819 Dihedral : 4.212 54.274 2149 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.52 % Allowed : 11.78 % Favored : 85.70 % 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: 0.39 (0.19), residues: 1925 helix: 0.83 (0.42), residues: 156 sheet: 1.11 (0.22), residues: 563 loop : -0.21 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 81 TYR 0.017 0.001 TYR I 86 PHE 0.020 0.001 PHE C 156 TRP 0.011 0.001 TRP K 33 HIS 0.006 0.002 HIS G 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (16155) covalent geometry : angle 0.53105 / 0.29 (21903) hydrogen bonds : bond 0.04689 / 3.09 ( 525) hydrogen bonds : angle 6.05896 / 4.12 ( 1368) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 307 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8453 (mt0) cc_final: 0.7999 (mt0) REVERT: A 802 GLU cc_start: 0.7546 (pt0) cc_final: 0.7303 (pt0) REVERT: A 869 MET cc_start: 0.8356 (tmm) cc_final: 0.7989 (tmm) REVERT: C 25 LEU cc_start: 0.8773 (tt) cc_final: 0.8566 (tt) REVERT: C 62 THR cc_start: 0.8820 (t) cc_final: 0.8516 (m) REVERT: C 83 LYS cc_start: 0.7131 (mttt) cc_final: 0.6734 (mttt) REVERT: C 85 TRP cc_start: 0.6929 (m100) cc_final: 0.6676 (m100) REVERT: C 148 LEU cc_start: 0.7489 (tp) cc_final: 0.7179 (pp) REVERT: C 166 LYS cc_start: 0.7092 (ttmt) cc_final: 0.6566 (tttt) REVERT: D 39 MET cc_start: 0.8258 (ttp) cc_final: 0.7159 (ttp) REVERT: D 75 THR cc_start: 0.9170 (m) cc_final: 0.8725 (p) REVERT: E 171 VAL cc_start: 0.8874 (t) cc_final: 0.8524 (t) REVERT: F 53 ILE cc_start: 0.8924 (mt) cc_final: 0.8445 (tt) REVERT: F 124 MET cc_start: 0.8115 (ptp) cc_final: 0.7665 (ptp) REVERT: F 167 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6869 (mm-30) REVERT: G 239 LEU cc_start: 0.7636 (mt) cc_final: 0.7318 (mp) REVERT: G 272 THR cc_start: 0.8777 (p) cc_final: 0.8390 (t) REVERT: G 304 THR cc_start: 0.8914 (m) cc_final: 0.8581 (p) REVERT: G 359 LEU cc_start: 0.9121 (mt) cc_final: 0.8685 (mt) REVERT: G 360 SER cc_start: 0.9191 (t) cc_final: 0.8932 (m) REVERT: G 375 VAL cc_start: 0.9232 (p) cc_final: 0.8946 (m) REVERT: G 406 LYS cc_start: 0.8024 (tttt) cc_final: 0.7246 (ttpt) REVERT: G 431 ILE cc_start: 0.9156 (tp) cc_final: 0.8845 (tt) REVERT: G 468 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.5299 (t80) REVERT: H 94 SER cc_start: 0.8057 (p) cc_final: 0.7681 (t) REVERT: H 172 ASN cc_start: 0.7767 (p0) cc_final: 0.7530 (p0) REVERT: I 49 LEU cc_start: 0.8359 (mt) cc_final: 0.7737 (mt) REVERT: I 82 ASN cc_start: 0.8893 (p0) cc_final: 0.8604 (p0) REVERT: I 103 TYR cc_start: 0.6100 (m-80) cc_final: 0.5879 (m-10) REVERT: I 118 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6312 (tt0) REVERT: I 151 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7713 (pt) REVERT: I 184 ARG cc_start: 0.6997 (ttp-170) cc_final: 0.5414 (tmt170) REVERT: J 52 ILE cc_start: 0.5818 (mm) cc_final: 0.5604 (mm) REVERT: J 134 THR cc_start: 0.8019 (m) cc_final: 0.7792 (m) REVERT: K 63 LEU cc_start: 0.6997 (mp) cc_final: 0.6756 (tp) REVERT: K 126 LEU cc_start: 0.7941 (tt) cc_final: 0.7660 (tp) outliers start: 45 outliers final: 19 residues processed: 332 average time/residue: 0.1112 time to fit residues: 58.6410 Evaluate side-chains 298 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 276 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 268 ASN Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 468 TYR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 28 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 24 optimal weight: 0.0870 chunk 13 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 156 optimal weight: 0.4980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 92 ASN I 96 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN J 397 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103508 restraints weight = 29468.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103554 restraints weight = 24894.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104108 restraints weight = 21416.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.104434 restraints weight = 18347.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104749 restraints weight = 16175.014| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16155 Z= 0.109 Angle : 0.528 11.764 21903 Z= 0.278 Chirality : 0.045 0.186 2419 Planarity : 0.004 0.050 2819 Dihedral : 4.017 16.469 2147 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.75 % Allowed : 12.68 % Favored : 84.58 % 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: 0.32 (0.19), residues: 1925 helix: 1.08 (0.42), residues: 150 sheet: 1.00 (0.22), residues: 559 loop : -0.25 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 118 TYR 0.018 0.001 TYR K 102 PHE 0.022 0.001 PHE C 156 TRP 0.012 0.001 TRP K 33 HIS 0.005 0.002 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (16155) covalent geometry : angle 0.52797 / 0.28 (21903) hydrogen bonds : bond 0.04143 / 2.73 ( 525) hydrogen bonds : angle 5.78223 / 3.93 ( 1368) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8476 (mt0) cc_final: 0.8225 (mt0) REVERT: A 869 MET cc_start: 0.8180 (tmm) cc_final: 0.7885 (tmm) REVERT: A 884 GLU cc_start: 0.5310 (OUTLIER) cc_final: 0.5043 (mt-10) REVERT: C 53 ILE cc_start: 0.9332 (mt) cc_final: 0.8881 (mm) REVERT: C 62 THR cc_start: 0.8813 (t) cc_final: 0.8564 (m) REVERT: C 83 LYS cc_start: 0.7086 (mttt) cc_final: 0.6674 (mttt) REVERT: C 85 TRP cc_start: 0.6975 (m100) cc_final: 0.6730 (m100) REVERT: C 148 LEU cc_start: 0.7524 (tp) cc_final: 0.7034 (pp) REVERT: C 166 LYS cc_start: 0.7171 (ttmt) cc_final: 0.6690 (tttt) REVERT: D 75 THR cc_start: 0.9192 (m) cc_final: 0.8780 (p) REVERT: E 171 VAL cc_start: 0.8869 (t) cc_final: 0.8494 (t) REVERT: F 124 MET cc_start: 0.7961 (ptp) cc_final: 0.7425 (ptp) REVERT: F 167 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6770 (mm-30) REVERT: G 239 LEU cc_start: 0.7625 (mt) cc_final: 0.7287 (mp) REVERT: G 272 THR cc_start: 0.8562 (p) cc_final: 0.8144 (t) REVERT: G 304 THR cc_start: 0.8924 (m) cc_final: 0.8582 (p) REVERT: G 359 LEU cc_start: 0.9133 (mt) cc_final: 0.8703 (mt) REVERT: G 360 SER cc_start: 0.9201 (t) cc_final: 0.8922 (m) REVERT: G 375 VAL cc_start: 0.9243 (p) cc_final: 0.8976 (m) REVERT: G 406 LYS cc_start: 0.8049 (tttt) cc_final: 0.7255 (ttpt) REVERT: G 431 ILE cc_start: 0.9192 (tp) cc_final: 0.8860 (tt) REVERT: G 468 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.5295 (t80) REVERT: H 94 SER cc_start: 0.8028 (p) cc_final: 0.7680 (t) REVERT: H 172 ASN cc_start: 0.7593 (p0) cc_final: 0.7372 (p0) REVERT: I 49 LEU cc_start: 0.8389 (mt) cc_final: 0.7780 (mt) REVERT: I 82 ASN cc_start: 0.8906 (p0) cc_final: 0.8570 (p0) REVERT: I 103 TYR cc_start: 0.6087 (m-80) cc_final: 0.5818 (m-10) REVERT: I 151 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7704 (pt) REVERT: I 184 ARG cc_start: 0.7005 (ttp-170) cc_final: 0.5465 (tmt170) REVERT: J 45 PHE cc_start: 0.6390 (m-80) cc_final: 0.6148 (m-80) REVERT: J 134 THR cc_start: 0.8017 (m) cc_final: 0.7779 (m) REVERT: K 63 LEU cc_start: 0.7012 (mp) cc_final: 0.6755 (tp) outliers start: 49 outliers final: 28 residues processed: 326 average time/residue: 0.1081 time to fit residues: 56.7636 Evaluate side-chains 287 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 468 TYR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 0.0970 chunk 120 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN D 61 GLN G 268 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN J 397 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100616 restraints weight = 29759.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100856 restraints weight = 24217.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101580 restraints weight = 21224.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.101852 restraints weight = 17489.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101994 restraints weight = 14987.578| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16155 Z= 0.143 Angle : 0.541 7.286 21903 Z= 0.288 Chirality : 0.046 0.171 2419 Planarity : 0.004 0.049 2819 Dihedral : 4.216 16.798 2147 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.20 % Allowed : 14.02 % Favored : 82.78 % 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: 0.14 (0.19), residues: 1925 helix: 0.88 (0.41), residues: 156 sheet: 0.92 (0.22), residues: 556 loop : -0.41 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 168 TYR 0.026 0.001 TYR K 102 PHE 0.025 0.002 PHE C 156 TRP 0.008 0.001 TRP I 398 HIS 0.006 0.002 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (16155) covalent geometry : angle 0.54123 / 0.29 (21903) hydrogen bonds : bond 0.04120 / 2.71 ( 525) hydrogen bonds : angle 5.64094 / 3.84 ( 1368) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 276 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8515 (mt0) cc_final: 0.8123 (mt0) REVERT: A 93 ASP cc_start: 0.7264 (p0) cc_final: 0.7034 (p0) REVERT: A 869 MET cc_start: 0.8263 (tmm) cc_final: 0.7958 (tmm) REVERT: B 23 VAL cc_start: 0.8758 (t) cc_final: 0.8438 (p) REVERT: C 83 LYS cc_start: 0.7106 (mttt) cc_final: 0.6729 (mttt) REVERT: C 110 ASP cc_start: 0.7238 (p0) cc_final: 0.6943 (t70) REVERT: C 148 LEU cc_start: 0.7479 (tp) cc_final: 0.7025 (pp) REVERT: D 39 MET cc_start: 0.8306 (ttp) cc_final: 0.7203 (ttp) REVERT: D 55 PHE cc_start: 0.8153 (m-80) cc_final: 0.7891 (m-80) REVERT: D 75 THR cc_start: 0.9121 (m) cc_final: 0.8827 (p) REVERT: E 171 VAL cc_start: 0.8852 (t) cc_final: 0.8460 (t) REVERT: F 53 ILE cc_start: 0.8775 (mt) cc_final: 0.8309 (tt) REVERT: F 124 MET cc_start: 0.8175 (ptp) cc_final: 0.7729 (ptp) REVERT: F 140 SER cc_start: 0.9148 (p) cc_final: 0.8758 (m) REVERT: F 167 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6969 (mm-30) REVERT: G 239 LEU cc_start: 0.7677 (mt) cc_final: 0.7305 (mp) REVERT: G 272 THR cc_start: 0.8586 (p) cc_final: 0.8163 (t) REVERT: G 304 THR cc_start: 0.8973 (m) cc_final: 0.8595 (p) REVERT: G 359 LEU cc_start: 0.9141 (mt) cc_final: 0.8814 (mt) REVERT: G 375 VAL cc_start: 0.9305 (p) cc_final: 0.8986 (m) REVERT: G 406 LYS cc_start: 0.8130 (tttt) cc_final: 0.7308 (ttpt) REVERT: G 431 ILE cc_start: 0.9198 (tp) cc_final: 0.8861 (tt) REVERT: G 468 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.5478 (t80) REVERT: H 94 SER cc_start: 0.8053 (p) cc_final: 0.7753 (t) REVERT: H 172 ASN cc_start: 0.7766 (p0) cc_final: 0.7429 (p0) REVERT: I 49 LEU cc_start: 0.8421 (mt) cc_final: 0.7813 (mt) REVERT: I 103 TYR cc_start: 0.6067 (m-80) cc_final: 0.5823 (m-10) REVERT: I 151 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7804 (pt) REVERT: I 184 ARG cc_start: 0.7180 (ttp-170) cc_final: 0.5624 (tmt170) REVERT: J 134 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7883 (m) REVERT: K 63 LEU cc_start: 0.7115 (mp) cc_final: 0.6801 (tp) REVERT: K 126 LEU cc_start: 0.8145 (tt) cc_final: 0.7783 (tp) REVERT: K 149 LEU cc_start: 0.7310 (tp) cc_final: 0.7085 (mp) outliers start: 57 outliers final: 41 residues processed: 308 average time/residue: 0.0922 time to fit residues: 45.5531 Evaluate side-chains 302 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 468 TYR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 108 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 136 optimal weight: 0.0170 chunk 167 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 98 optimal weight: 0.0000 chunk 92 optimal weight: 2.9990 overall best weight: 1.6028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 92 ASN G 268 ASN G 303 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099331 restraints weight = 29799.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099309 restraints weight = 25834.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.099681 restraints weight = 23068.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.099888 restraints weight = 20390.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.100110 restraints weight = 18434.167| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16155 Z= 0.175 Angle : 0.561 6.648 21903 Z= 0.300 Chirality : 0.046 0.171 2419 Planarity : 0.004 0.050 2819 Dihedral : 4.425 18.912 2147 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.93 % Allowed : 14.25 % Favored : 81.83 % 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: -0.07 (0.18), residues: 1925 helix: 0.82 (0.42), residues: 150 sheet: 0.75 (0.22), residues: 556 loop : -0.54 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 168 TYR 0.026 0.002 TYR K 102 PHE 0.026 0.002 PHE C 156 TRP 0.014 0.002 TRP J 398 HIS 0.005 0.002 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (16155) covalent geometry : angle 0.56056 / 0.30 (21903) hydrogen bonds : bond 0.04162 / 2.74 ( 525) hydrogen bonds : angle 5.65600 / 3.85 ( 1368) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 256 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8522 (mt0) cc_final: 0.7950 (mt0) REVERT: A 869 MET cc_start: 0.8313 (tmm) cc_final: 0.8006 (tmm) REVERT: B 23 VAL cc_start: 0.8766 (t) cc_final: 0.8475 (p) REVERT: C 83 LYS cc_start: 0.7071 (mttt) cc_final: 0.6680 (mttt) REVERT: C 148 LEU cc_start: 0.7900 (tp) cc_final: 0.7081 (pp) REVERT: D 11 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8207 (mp) REVERT: D 39 MET cc_start: 0.8271 (ttp) cc_final: 0.7009 (ttp) REVERT: D 75 THR cc_start: 0.9156 (m) cc_final: 0.8858 (p) REVERT: E 171 VAL cc_start: 0.8882 (t) cc_final: 0.8490 (t) REVERT: F 53 ILE cc_start: 0.8823 (mt) cc_final: 0.8326 (tt) REVERT: F 124 MET cc_start: 0.8219 (ptp) cc_final: 0.7791 (ptp) REVERT: F 140 SER cc_start: 0.9052 (p) cc_final: 0.8573 (m) REVERT: F 167 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6968 (mm-30) REVERT: G 239 LEU cc_start: 0.7688 (mt) cc_final: 0.7305 (mp) REVERT: G 301 ASN cc_start: 0.5681 (p0) cc_final: 0.5018 (p0) REVERT: G 304 THR cc_start: 0.9072 (m) cc_final: 0.8655 (p) REVERT: G 359 LEU cc_start: 0.9151 (mt) cc_final: 0.8755 (mt) REVERT: G 360 SER cc_start: 0.9199 (t) cc_final: 0.8975 (m) REVERT: G 375 VAL cc_start: 0.9331 (p) cc_final: 0.8981 (m) REVERT: G 406 LYS cc_start: 0.8168 (tttt) cc_final: 0.7325 (ttpt) REVERT: G 431 ILE cc_start: 0.9203 (tp) cc_final: 0.8879 (tt) REVERT: G 439 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8373 (mtm) REVERT: G 468 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.6246 (m-80) REVERT: H 94 SER cc_start: 0.8046 (p) cc_final: 0.7765 (t) REVERT: H 172 ASN cc_start: 0.7968 (p0) cc_final: 0.7560 (p0) REVERT: I 49 LEU cc_start: 0.8437 (mt) cc_final: 0.7844 (mt) REVERT: I 103 TYR cc_start: 0.6043 (m-80) cc_final: 0.5789 (m-10) REVERT: I 151 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7842 (pt) REVERT: I 184 ARG cc_start: 0.7311 (ttp-170) cc_final: 0.5681 (tmt170) REVERT: J 134 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.7977 (m) outliers start: 70 outliers final: 47 residues processed: 299 average time/residue: 0.0964 time to fit residues: 46.0589 Evaluate side-chains 297 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 245 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 890 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 309 MET Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 468 TYR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 152 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 60 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN G 389 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN J 397 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.098770 restraints weight = 29624.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.098504 restraints weight = 27001.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.099240 restraints weight = 24566.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099426 restraints weight = 19113.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.099578 restraints weight = 17571.087| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16155 Z= 0.165 Angle : 0.556 6.630 21903 Z= 0.297 Chirality : 0.046 0.170 2419 Planarity : 0.004 0.050 2819 Dihedral : 4.521 19.372 2147 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.81 % Allowed : 14.92 % Favored : 81.27 % 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: -0.24 (0.18), residues: 1925 helix: 0.57 (0.41), residues: 164 sheet: 0.67 (0.21), residues: 553 loop : -0.67 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 325 TYR 0.028 0.002 TYR K 102 PHE 0.025 0.002 PHE C 156 TRP 0.008 0.001 TRP I 398 HIS 0.005 0.002 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (16155) covalent geometry : angle 0.55574 / 0.30 (21903) hydrogen bonds : bond 0.04066 / 2.67 ( 525) hydrogen bonds : angle 5.64799 / 3.85 ( 1368) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 273 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8593 (mt0) cc_final: 0.7866 (mt0) REVERT: B 23 VAL cc_start: 0.8773 (t) cc_final: 0.8482 (p) REVERT: C 83 LYS cc_start: 0.7101 (mttt) cc_final: 0.6688 (mttt) REVERT: C 148 LEU cc_start: 0.8415 (tp) cc_final: 0.7305 (pp) REVERT: C 166 LYS cc_start: 0.7203 (ttmt) cc_final: 0.6684 (tttt) REVERT: D 11 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8425 (mp) REVERT: D 39 MET cc_start: 0.8277 (ttp) cc_final: 0.6978 (ttp) REVERT: D 61 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7745 (mm-40) REVERT: D 75 THR cc_start: 0.9170 (m) cc_final: 0.8870 (p) REVERT: D 124 LEU cc_start: 0.8421 (mt) cc_final: 0.8211 (mp) REVERT: E 80 TYR cc_start: 0.8385 (p90) cc_final: 0.8184 (p90) REVERT: E 171 VAL cc_start: 0.8884 (t) cc_final: 0.8485 (t) REVERT: F 124 MET cc_start: 0.8189 (ptp) cc_final: 0.7851 (ptp) REVERT: F 140 SER cc_start: 0.9037 (p) cc_final: 0.8575 (m) REVERT: F 167 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6918 (mm-30) REVERT: G 301 ASN cc_start: 0.5879 (p0) cc_final: 0.5481 (p0) REVERT: G 304 THR cc_start: 0.9074 (m) cc_final: 0.8683 (p) REVERT: G 359 LEU cc_start: 0.9135 (mt) cc_final: 0.8756 (mt) REVERT: G 375 VAL cc_start: 0.9335 (p) cc_final: 0.8987 (m) REVERT: G 406 LYS cc_start: 0.8223 (tttt) cc_final: 0.7319 (ttpt) REVERT: G 431 ILE cc_start: 0.9188 (tp) cc_final: 0.8893 (tt) REVERT: G 439 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8333 (mtm) REVERT: G 468 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.6082 (m-80) REVERT: H 94 SER cc_start: 0.8076 (p) cc_final: 0.7831 (t) REVERT: H 160 GLU cc_start: 0.6815 (tt0) cc_final: 0.6509 (tt0) REVERT: H 172 ASN cc_start: 0.7969 (p0) cc_final: 0.7417 (p0) REVERT: I 49 LEU cc_start: 0.8457 (mt) cc_final: 0.7882 (mt) REVERT: I 103 TYR cc_start: 0.6132 (m-80) cc_final: 0.5872 (m-10) REVERT: I 151 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.7823 (pt) REVERT: I 184 ARG cc_start: 0.7390 (ttp-170) cc_final: 0.5736 (tmt170) REVERT: J 134 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8074 (m) REVERT: K 126 LEU cc_start: 0.7632 (tt) cc_final: 0.7211 (tp) outliers start: 68 outliers final: 49 residues processed: 313 average time/residue: 0.0972 time to fit residues: 49.4730 Evaluate side-chains 313 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 259 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 890 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 309 MET Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 468 TYR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 152 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 94 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 GLN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.099541 restraints weight = 29712.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099389 restraints weight = 27756.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.100027 restraints weight = 23962.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.100263 restraints weight = 20276.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.100379 restraints weight = 18098.182| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16155 Z= 0.125 Angle : 0.537 6.683 21903 Z= 0.286 Chirality : 0.045 0.172 2419 Planarity : 0.004 0.131 2819 Dihedral : 4.432 18.500 2147 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.14 % Allowed : 15.82 % Favored : 81.04 % 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: -0.17 (0.18), residues: 1925 helix: 0.92 (0.42), residues: 158 sheet: 0.66 (0.21), residues: 556 loop : -0.63 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 77 TYR 0.012 0.001 TYR A 133 PHE 0.027 0.001 PHE C 156 TRP 0.026 0.001 TRP J 398 HIS 0.004 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (16155) covalent geometry : angle 0.53735 / 0.29 (21903) hydrogen bonds : bond 0.03907 / 2.59 ( 525) hydrogen bonds : angle 5.56748 / 3.79 ( 1368) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8581 (mt0) cc_final: 0.7811 (mt0) REVERT: A 869 MET cc_start: 0.8075 (tmm) cc_final: 0.7834 (tmm) REVERT: A 884 GLU cc_start: 0.5380 (OUTLIER) cc_final: 0.5087 (mt-10) REVERT: B 23 VAL cc_start: 0.8778 (t) cc_final: 0.8485 (p) REVERT: C 83 LYS cc_start: 0.7177 (mttt) cc_final: 0.6769 (mttt) REVERT: C 148 LEU cc_start: 0.8431 (tp) cc_final: 0.7315 (pp) REVERT: D 11 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8252 (mp) REVERT: D 39 MET cc_start: 0.8427 (ttp) cc_final: 0.7609 (ttp) REVERT: D 75 THR cc_start: 0.9130 (m) cc_final: 0.8839 (p) REVERT: D 124 LEU cc_start: 0.8430 (mt) cc_final: 0.8220 (mp) REVERT: E 168 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7732 (ptt180) REVERT: E 171 VAL cc_start: 0.8891 (t) cc_final: 0.8505 (t) REVERT: F 91 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6839 (tm-30) REVERT: F 124 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7713 (ptp) REVERT: F 140 SER cc_start: 0.8861 (p) cc_final: 0.8523 (m) REVERT: F 167 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6781 (mm-30) REVERT: G 304 THR cc_start: 0.9046 (m) cc_final: 0.8678 (p) REVERT: G 359 LEU cc_start: 0.9110 (mt) cc_final: 0.8709 (mt) REVERT: G 375 VAL cc_start: 0.9325 (p) cc_final: 0.8981 (m) REVERT: G 385 THR cc_start: 0.8677 (m) cc_final: 0.8283 (p) REVERT: G 406 LYS cc_start: 0.8192 (tttt) cc_final: 0.7314 (ttpt) REVERT: G 431 ILE cc_start: 0.9178 (tp) cc_final: 0.8829 (tt) REVERT: G 439 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8466 (mtm) REVERT: G 468 TYR cc_start: 0.6826 (OUTLIER) cc_final: 0.5623 (m-80) REVERT: H 94 SER cc_start: 0.8052 (p) cc_final: 0.7808 (t) REVERT: H 172 ASN cc_start: 0.7904 (p0) cc_final: 0.7453 (p0) REVERT: I 49 LEU cc_start: 0.8469 (mt) cc_final: 0.7883 (mt) REVERT: I 103 TYR cc_start: 0.6056 (m-80) cc_final: 0.5806 (m-10) REVERT: I 151 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7779 (pt) REVERT: I 184 ARG cc_start: 0.7372 (ttp-170) cc_final: 0.5745 (tmt170) REVERT: J 78 LEU cc_start: 0.7610 (tp) cc_final: 0.7288 (mt) REVERT: K 126 LEU cc_start: 0.7693 (tt) cc_final: 0.7216 (tp) outliers start: 56 outliers final: 43 residues processed: 299 average time/residue: 0.0932 time to fit residues: 45.2735 Evaluate side-chains 305 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 468 TYR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 152 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 85 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 chunk 129 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.0020 chunk 126 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN J 397 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100433 restraints weight = 29580.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100418 restraints weight = 25519.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101444 restraints weight = 22289.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.101566 restraints weight = 18696.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101696 restraints weight = 15814.281| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16155 Z= 0.109 Angle : 0.524 5.971 21903 Z= 0.281 Chirality : 0.045 0.167 2419 Planarity : 0.004 0.077 2819 Dihedral : 4.304 16.847 2147 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.92 % Allowed : 16.43 % Favored : 80.65 % 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: -0.09 (0.18), residues: 1925 helix: 1.08 (0.42), residues: 158 sheet: 0.71 (0.21), residues: 557 loop : -0.59 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 77 TYR 0.010 0.001 TYR F 55 PHE 0.026 0.001 PHE C 156 TRP 0.011 0.001 TRP K 33 HIS 0.004 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (16155) covalent geometry : angle 0.52419 / 0.28 (21903) hydrogen bonds : bond 0.03674 / 2.43 ( 525) hydrogen bonds : angle 5.47002 / 3.72 ( 1368) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 0.436 Fit side-chains REVERT: A 40 GLN cc_start: 0.8587 (mt0) cc_final: 0.7799 (mt0) REVERT: A 869 MET cc_start: 0.8031 (tmm) cc_final: 0.7824 (tmm) REVERT: A 884 GLU cc_start: 0.5164 (OUTLIER) cc_final: 0.4913 (mt-10) REVERT: B 23 VAL cc_start: 0.8761 (t) cc_final: 0.8458 (p) REVERT: C 83 LYS cc_start: 0.7186 (mttt) cc_final: 0.6754 (mttt) REVERT: C 148 LEU cc_start: 0.8347 (tp) cc_final: 0.7171 (pp) REVERT: C 166 LYS cc_start: 0.6859 (ttmm) cc_final: 0.6234 (tptt) REVERT: D 11 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8384 (mp) REVERT: D 24 LEU cc_start: 0.8983 (mt) cc_final: 0.8728 (mp) REVERT: D 39 MET cc_start: 0.8105 (ttp) cc_final: 0.7292 (ttp) REVERT: D 75 THR cc_start: 0.9121 (m) cc_final: 0.8802 (p) REVERT: D 104 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7091 (mm-30) REVERT: E 53 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8375 (mt) REVERT: E 171 VAL cc_start: 0.8900 (t) cc_final: 0.8502 (t) REVERT: F 62 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8845 (t) REVERT: F 91 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6753 (tm-30) REVERT: F 124 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7688 (ptp) REVERT: F 140 SER cc_start: 0.8850 (p) cc_final: 0.8526 (m) REVERT: G 304 THR cc_start: 0.9025 (m) cc_final: 0.8688 (p) REVERT: G 359 LEU cc_start: 0.9106 (mt) cc_final: 0.8695 (mt) REVERT: G 375 VAL cc_start: 0.9331 (p) cc_final: 0.8978 (m) REVERT: G 385 THR cc_start: 0.8616 (m) cc_final: 0.8261 (p) REVERT: G 406 LYS cc_start: 0.8167 (tttt) cc_final: 0.7305 (ttpt) REVERT: G 431 ILE cc_start: 0.9168 (tp) cc_final: 0.8814 (tt) REVERT: G 439 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8296 (mtm) REVERT: G 468 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.5608 (m-80) REVERT: H 172 ASN cc_start: 0.7746 (p0) cc_final: 0.7355 (p0) REVERT: H 182 MET cc_start: 0.6826 (ttp) cc_final: 0.6492 (tpt) REVERT: I 49 LEU cc_start: 0.8235 (mt) cc_final: 0.7839 (mt) REVERT: I 103 TYR cc_start: 0.5978 (m-80) cc_final: 0.5726 (m-10) REVERT: I 151 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7754 (pt) REVERT: I 184 ARG cc_start: 0.7424 (ttp-170) cc_final: 0.5749 (tmt170) REVERT: K 126 LEU cc_start: 0.7700 (tt) cc_final: 0.7230 (tp) outliers start: 52 outliers final: 38 residues processed: 308 average time/residue: 0.0861 time to fit residues: 42.9496 Evaluate side-chains 299 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 468 TYR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 152 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 70 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 84 ASN C 119 GLN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN J 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.098898 restraints weight = 29755.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098792 restraints weight = 26742.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099167 restraints weight = 23591.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.099507 restraints weight = 20693.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.099546 restraints weight = 19025.613| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16155 Z= 0.165 Angle : 0.572 8.074 21903 Z= 0.305 Chirality : 0.046 0.177 2419 Planarity : 0.004 0.075 2819 Dihedral : 4.494 18.304 2147 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.97 % Allowed : 16.60 % Favored : 80.43 % 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: -0.28 (0.18), residues: 1925 helix: 0.71 (0.41), residues: 164 sheet: 0.62 (0.21), residues: 560 loop : -0.72 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 168 TYR 0.015 0.002 TYR B 90 PHE 0.031 0.002 PHE C 150 TRP 0.009 0.002 TRP C 100 HIS 0.005 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (16155) covalent geometry : angle 0.57209 / 0.30 (21903) hydrogen bonds : bond 0.03940 / 2.59 ( 525) hydrogen bonds : angle 5.56850 / 3.79 ( 1368) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 265 time to evaluate : 0.614 Fit side-chains REVERT: A 40 GLN cc_start: 0.8623 (mt0) cc_final: 0.7860 (mt0) REVERT: A 884 GLU cc_start: 0.5295 (OUTLIER) cc_final: 0.5012 (mt-10) REVERT: B 23 VAL cc_start: 0.8772 (t) cc_final: 0.8488 (p) REVERT: C 83 LYS cc_start: 0.7163 (mttt) cc_final: 0.6740 (mttt) REVERT: C 148 LEU cc_start: 0.8324 (tp) cc_final: 0.7236 (pp) REVERT: D 11 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8268 (mp) REVERT: D 24 LEU cc_start: 0.8961 (mt) cc_final: 0.8676 (mp) REVERT: D 39 MET cc_start: 0.8377 (ttp) cc_final: 0.7537 (ttp) REVERT: E 53 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8410 (mt) REVERT: E 171 VAL cc_start: 0.8908 (t) cc_final: 0.8510 (t) REVERT: F 124 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7748 (ptp) REVERT: F 140 SER cc_start: 0.8993 (p) cc_final: 0.8630 (m) REVERT: G 304 THR cc_start: 0.9069 (m) cc_final: 0.8709 (p) REVERT: G 360 SER cc_start: 0.9189 (t) cc_final: 0.8954 (m) REVERT: G 375 VAL cc_start: 0.9334 (p) cc_final: 0.8966 (m) REVERT: G 406 LYS cc_start: 0.8206 (tttt) cc_final: 0.7355 (ttpt) REVERT: G 431 ILE cc_start: 0.9170 (tp) cc_final: 0.8831 (tt) REVERT: G 439 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8394 (mtm) REVERT: G 468 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.5732 (m-80) REVERT: H 172 ASN cc_start: 0.8001 (p0) cc_final: 0.7542 (p0) REVERT: I 49 LEU cc_start: 0.8258 (mt) cc_final: 0.7834 (mt) REVERT: I 103 TYR cc_start: 0.6268 (m-80) cc_final: 0.6029 (m-10) REVERT: I 151 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7800 (pt) REVERT: I 184 ARG cc_start: 0.7516 (ttp-170) cc_final: 0.5798 (tmt170) REVERT: K 126 LEU cc_start: 0.7738 (tt) cc_final: 0.7255 (tp) outliers start: 53 outliers final: 40 residues processed: 302 average time/residue: 0.0898 time to fit residues: 43.9055 Evaluate side-chains 298 residues out of total 1783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 150 PHE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 439 MET Chi-restraints excluded: chain G residue 468 TYR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 397 ASN Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 152 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 104 optimal weight: 0.0270 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN J 397 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.098565 restraints weight = 29704.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.098688 restraints weight = 25520.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.099164 restraints weight = 22360.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.099410 restraints weight = 20726.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.099507 restraints weight = 17506.421| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.260 16155 Z= 0.251 Angle : 0.781 59.165 21903 Z= 0.439 Chirality : 0.053 1.366 2419 Planarity : 0.005 0.077 2819 Dihedral : 4.502 18.475 2147 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.75 % Allowed : 17.11 % Favored : 80.15 % Cbeta Deviations : 0.05 % 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: -0.29 (0.18), residues: 1925 helix: 0.71 (0.41), residues: 164 sheet: 0.62 (0.21), residues: 560 loop : -0.72 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 168 TYR 0.018 0.001 TYR K 117 PHE 0.024 0.002 PHE C 150 TRP 0.008 0.001 TRP I 398 HIS 0.004 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.25 (16155) covalent geometry : angle 0.78113 / 0.44 (21903) hydrogen bonds : bond 0.03938 / 2.59 ( 525) hydrogen bonds : angle 5.56763 / 3.79 ( 1368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2295.11 seconds wall clock time: 40 minutes 51.05 seconds (2451.05 seconds total)