Starting phenix.real_space_refine on Mon Jun 23 18:05:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kiv_9999/06_2025/6kiv_9999.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kiv_9999/06_2025/6kiv_9999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kiv_9999/06_2025/6kiv_9999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kiv_9999/06_2025/6kiv_9999.map" model { file = "/net/cci-nas-00/data/ceres_data/6kiv_9999/06_2025/6kiv_9999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kiv_9999/06_2025/6kiv_9999.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8596 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 290 5.49 5 S 61 5.16 5 C 12166 2.51 5 N 3759 2.21 5 O 4442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20719 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "D" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1434 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2881 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 14, 'TRANS': 351} Chain breaks: 1 Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "T" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1399 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 12, 'TRANS': 163} Chain breaks: 1 Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2326 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13389 SG CYS K3957 39.155 70.820 42.538 1.00167.86 S ATOM 13403 SG CYS K3959 42.422 71.072 44.036 1.00163.71 S Time building chain proxies: 10.89, per 1000 atoms: 0.53 Number of scatterers: 20719 At special positions: 0 Unit cell: (151.51, 141.7, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 61 16.00 P 290 15.00 O 4442 8.00 N 3759 7.00 C 12166 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3957 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 35 sheets defined 31.8% alpha, 13.0% beta 145 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 9.51 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.554A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.997A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.858A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.671A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.917A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.843A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 4.083A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.201A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.554A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.997A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.672A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 4.145A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.461A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.771A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.664A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 4.034A pdb=" N ALA H 121 " --> pdb=" O CYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 3815 through 3830 removed outlier: 3.755A pdb=" N ARG K3819 " --> pdb=" O PRO K3815 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS K3828 " --> pdb=" O LYS K3824 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU K3829 " --> pdb=" O LYS K3825 " (cutoff:3.500A) Processing helix chain 'K' and resid 3866 through 3878 removed outlier: 4.719A pdb=" N LYS K3870 " --> pdb=" O ILE K3866 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'O' and resid 22 through 34 removed outlier: 3.827A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 41 removed outlier: 4.187A pdb=" N GLN O 41 " --> pdb=" O PRO O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 59 removed outlier: 3.536A pdb=" N ASP O 58 " --> pdb=" O THR O 55 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR O 59 " --> pdb=" O LEU O 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 59' Processing helix chain 'T' and resid 501 through 503 No H-bonds generated for 'chain 'T' and resid 501 through 503' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.620A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.424A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.396A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.116A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.816A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'K' and resid 3831 through 3835 removed outlier: 4.089A pdb=" N GLY K3832 " --> pdb=" O PHE K3844 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 3884 through 3886 Processing sheet with id=AA8, first strand: chain 'K' and resid 3898 through 3899 removed outlier: 3.608A pdb=" N GLY K3899 " --> pdb=" O LYS N 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 3906 through 3907 removed outlier: 6.746A pdb=" N ASN K3906 " --> pdb=" O TYR K3942 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 3915 through 3920 removed outlier: 3.951A pdb=" N ARG K3916 " --> pdb=" O VAL K3927 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL K3927 " --> pdb=" O ARG K3916 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE K3918 " --> pdb=" O HIS K3925 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS K3925 " --> pdb=" O ILE K3918 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE K3920 " --> pdb=" O GLN K3923 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN K3923 " --> pdb=" O ILE K3920 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'N' and resid 30 through 32 removed outlier: 3.586A pdb=" N THR N 31 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 69 through 73 removed outlier: 3.852A pdb=" N SER N 71 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA N 84 " --> pdb=" O SER N 71 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER N 83 " --> pdb=" O SER N 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 113 through 115 removed outlier: 3.790A pdb=" N GLN N 114 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL N 123 " --> pdb=" O LEU N 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.540A pdb=" N THR N 168 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 201 through 205 removed outlier: 7.131A pdb=" N ASN N 216 " --> pdb=" O LYS N 202 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE N 204 " --> pdb=" O LEU N 214 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU N 214 " --> pdb=" O ILE N 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 254 through 259 removed outlier: 6.977A pdb=" N GLY N 269 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N CYS N 257 " --> pdb=" O VAL N 267 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL N 267 " --> pdb=" O CYS N 257 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE N 259 " --> pdb=" O TYR N 265 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR N 265 " --> pdb=" O PHE N 259 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU N 276 " --> pdb=" O ILE N 289 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE N 289 " --> pdb=" O LEU N 276 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE N 278 " --> pdb=" O VAL N 287 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 310 through 311 removed outlier: 3.968A pdb=" N ILE N 310 " --> pdb=" O TRP N 321 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP N 321 " --> pdb=" O ILE N 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'O' and resid 12 through 16 removed outlier: 8.104A pdb=" N LEU O 67 " --> pdb=" O GLN O 2 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 43 through 45 removed outlier: 4.114A pdb=" N LEU O 43 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 306 through 308 removed outlier: 3.722A pdb=" N VAL T 480 " --> pdb=" O VAL T 307 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 314 through 316 removed outlier: 3.545A pdb=" N VAL T 316 " --> pdb=" O ILE T 472 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 396 through 398 removed outlier: 4.781A pdb=" N ILE T 396 " --> pdb=" O TRP T 327 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP T 327 " --> pdb=" O ILE T 396 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU T 398 " --> pdb=" O GLY T 325 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY T 325 " --> pdb=" O LEU T 398 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA T 326 " --> pdb=" O ARG T 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'T' and resid 331 through 332 Processing sheet with id=AC6, first strand: chain 'T' and resid 346 through 347 Processing sheet with id=AC7, first strand: chain 'T' and resid 372 through 374 removed outlier: 3.581A pdb=" N LYS T 380 " --> pdb=" O LYS T 373 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 448 through 450 removed outlier: 4.483A pdb=" N GLY T 457 " --> pdb=" O PHE T 449 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 36 through 37 Processing sheet with id=AD1, first strand: chain 'R' and resid 41 through 42 Processing sheet with id=AD2, first strand: chain 'R' and resid 48 through 53 removed outlier: 4.260A pdb=" N LYS R 52 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA R 61 " --> pdb=" O LYS R 52 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS R 70 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU R 68 " --> pdb=" O SER R 64 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 90 through 93 removed outlier: 3.783A pdb=" N ASP R 92 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS R 112 " --> pdb=" O SER R 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 136 through 137 removed outlier: 3.700A pdb=" N ASN R 136 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 177 through 179 removed outlier: 6.091A pdb=" N CYS R 195 " --> pdb=" O THR R 208 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR R 208 " --> pdb=" O CYS R 195 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE R 197 " --> pdb=" O LEU R 206 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 219 through 222 removed outlier: 3.615A pdb=" N LYS R 239 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 264 through 266 Processing sheet with id=AD8, first strand: chain 'R' and resid 304 through 309 removed outlier: 3.519A pdb=" N ALA R 308 " --> pdb=" O ALA R 317 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1506 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 9.76 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4052 1.33 - 1.45: 6267 1.45 - 1.57: 10731 1.57 - 1.69: 578 1.69 - 1.81: 88 Bond restraints: 21716 Sorted by residual: bond pdb=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.375 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" C2 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.330 1.378 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C6 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.338 1.386 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.491 -0.069 3.00e-02 1.11e+03 5.28e+00 ... (remaining 21711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 29917 2.52 - 5.04: 609 5.04 - 7.55: 44 7.55 - 10.07: 13 10.07 - 12.59: 2 Bond angle restraints: 30585 Sorted by residual: angle pdb=" CG SAH K4001 " pdb=" SD SAH K4001 " pdb=" C5' SAH K4001 " ideal model delta sigma weight residual 101.77 89.61 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 122.48 -9.30 2.37e+00 1.78e-01 1.54e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 125.89 -5.69 1.50e+00 4.44e-01 1.44e+01 angle pdb=" CA ARG G 99 " pdb=" CB ARG G 99 " pdb=" CG ARG G 99 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N GLN N 323 " pdb=" CA GLN N 323 " pdb=" C GLN N 323 " ideal model delta sigma weight residual 110.80 118.14 -7.34 2.13e+00 2.20e-01 1.19e+01 ... (remaining 30580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 10875 35.82 - 71.65: 1373 71.65 - 107.47: 25 107.47 - 143.29: 4 143.29 - 179.11: 1 Dihedral angle restraints: 12278 sinusoidal: 6877 harmonic: 5401 Sorted by residual: dihedral pdb=" CA LYS B 31 " pdb=" C LYS B 31 " pdb=" N PRO B 32 " pdb=" CA PRO B 32 " ideal model delta harmonic sigma weight residual 180.00 133.83 46.17 0 5.00e+00 4.00e-02 8.53e+01 dihedral pdb=" CA ASN K3779 " pdb=" C ASN K3779 " pdb=" N PHE K3780 " pdb=" CA PHE K3780 " ideal model delta harmonic sigma weight residual 180.00 138.88 41.12 0 5.00e+00 4.00e-02 6.76e+01 dihedral pdb=" CA TYR N 13 " pdb=" C TYR N 13 " pdb=" N PRO N 14 " pdb=" CA PRO N 14 " ideal model delta harmonic sigma weight residual -180.00 -143.60 -36.40 0 5.00e+00 4.00e-02 5.30e+01 ... (remaining 12275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2253 0.046 - 0.092: 872 0.092 - 0.138: 258 0.138 - 0.184: 49 0.184 - 0.230: 6 Chirality restraints: 3438 Sorted by residual: chirality pdb=" C1' SAH K4001 " pdb=" C2' SAH K4001 " pdb=" N9 SAH K4001 " pdb=" O4' SAH K4001 " both_signs ideal model delta sigma weight residual False 2.35 2.58 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3435 not shown) Planarity restraints: 2870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO B 32 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN K3779 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" CG ASN K3779 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN K3779 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN K3779 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K3768 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C VAL K3768 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL K3768 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS K3769 " -0.015 2.00e-02 2.50e+03 ... (remaining 2867 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4488 2.79 - 3.32: 17385 3.32 - 3.85: 37394 3.85 - 4.37: 41446 4.37 - 4.90: 64179 Nonbonded interactions: 164892 Sorted by model distance: nonbonded pdb=" OG SER R 129 " pdb=" OD2 ASP R 150 " model vdw 2.263 3.040 nonbonded pdb=" OG SER R 96 " pdb=" OD1 ASP R 98 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.265 3.040 nonbonded pdb=" OG SER R 49 " pdb=" O SER R 63 " model vdw 2.268 3.040 ... (remaining 164887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = (chain 'H' and resid 28 through 120) } 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 56.520 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 21720 Z= 0.328 Angle : 0.904 12.590 30585 Z= 0.511 Chirality : 0.053 0.230 3438 Planarity : 0.007 0.108 2870 Dihedral : 22.703 179.114 8794 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.16), residues: 1830 helix: -1.38 (0.17), residues: 568 sheet: -2.89 (0.26), residues: 312 loop : -3.18 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP N 303 HIS 0.010 0.002 HIS B 75 PHE 0.023 0.003 PHE N 189 TYR 0.031 0.003 TYR B 51 ARG 0.009 0.001 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.15019 ( 898) hydrogen bonds : angle 6.04261 ( 2250) metal coordination : bond 0.21670 ( 2) covalent geometry : bond 0.00716 (21716) covalent geometry : angle 0.90391 (30585) Misc. bond : bond 0.00378 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 2.025 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 58 THR cc_start: 0.9254 (p) cc_final: 0.8948 (p) REVERT: A 123 ASP cc_start: 0.8318 (m-30) cc_final: 0.8094 (m-30) REVERT: B 35 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8090 (ttm-80) REVERT: B 58 LEU cc_start: 0.8871 (tp) cc_final: 0.8573 (tt) REVERT: B 92 ARG cc_start: 0.8717 (mtp-110) cc_final: 0.8398 (mtp-110) REVERT: D 27 ARG cc_start: 0.7875 (tmt170) cc_final: 0.7629 (tmt-80) REVERT: D 54 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8811 (mmmm) REVERT: D 65 ASP cc_start: 0.8143 (t0) cc_final: 0.7866 (t0) REVERT: D 81 ASN cc_start: 0.8438 (m-40) cc_final: 0.8148 (m110) REVERT: D 88 SER cc_start: 0.9070 (p) cc_final: 0.8866 (p) REVERT: F 88 TYR cc_start: 0.8891 (m-10) cc_final: 0.7805 (m-10) REVERT: G 18 SER cc_start: 0.8315 (m) cc_final: 0.7614 (p) REVERT: G 42 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7727 (mtm-85) REVERT: G 61 GLU cc_start: 0.8672 (tp30) cc_final: 0.8331 (tm-30) REVERT: H 73 GLU cc_start: 0.8267 (tp30) cc_final: 0.8037 (mt-10) REVERT: H 80 TYR cc_start: 0.7333 (m-10) cc_final: 0.6582 (m-10) REVERT: H 82 LYS cc_start: 0.8942 (mttt) cc_final: 0.8089 (mmtt) REVERT: K 3828 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8215 (pttt) REVERT: K 3846 LYS cc_start: 0.6392 (mtmt) cc_final: 0.6074 (tmtt) REVERT: N 60 LYS cc_start: 0.8170 (tptt) cc_final: 0.7547 (tppt) REVERT: N 115 TYR cc_start: 0.5656 (m-80) cc_final: 0.5121 (m-10) REVERT: N 226 ASP cc_start: 0.7903 (t0) cc_final: 0.7649 (t0) REVERT: N 320 ILE cc_start: 0.8932 (mp) cc_final: 0.8636 (pt) REVERT: T 503 MET cc_start: 0.6152 (mmm) cc_final: 0.5486 (mtm) REVERT: R 72 TRP cc_start: 0.6754 (m100) cc_final: 0.5447 (m100) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.4432 time to fit residues: 315.7868 Evaluate side-chains 290 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 20.0000 chunk 157 optimal weight: 0.0050 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 63 optimal weight: 0.0040 chunk 99 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 188 optimal weight: 20.0000 overall best weight: 1.7610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS C 38 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 81 ASN F 25 ASN G 89 ASN G 110 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 HIS N 273 GLN N 328 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 375 HIS T 381 HIS ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.140911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.106514 restraints weight = 53070.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.106336 restraints weight = 34982.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107235 restraints weight = 28803.121| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21720 Z= 0.168 Angle : 0.655 12.495 30585 Z= 0.369 Chirality : 0.041 0.159 3438 Planarity : 0.005 0.085 2870 Dihedral : 27.576 177.847 5203 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.26 % Allowed : 10.97 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.18), residues: 1830 helix: 0.60 (0.21), residues: 573 sheet: -2.54 (0.27), residues: 296 loop : -2.95 (0.17), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 156 HIS 0.013 0.001 HIS R 44 PHE 0.019 0.002 PHE N 189 TYR 0.027 0.002 TYR B 51 ARG 0.005 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.05096 ( 898) hydrogen bonds : angle 4.05738 ( 2250) metal coordination : bond 0.00371 ( 2) covalent geometry : bond 0.00364 (21716) covalent geometry : angle 0.65497 (30585) Misc. bond : bond 0.00168 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 347 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8837 (t0) REVERT: D 88 SER cc_start: 0.8943 (p) cc_final: 0.8664 (p) REVERT: E 73 GLU cc_start: 0.8101 (tt0) cc_final: 0.7649 (tt0) REVERT: F 25 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7582 (t0) REVERT: F 64 ASN cc_start: 0.8544 (t0) cc_final: 0.8302 (t0) REVERT: F 88 TYR cc_start: 0.8797 (m-10) cc_final: 0.8416 (m-10) REVERT: H 82 LYS cc_start: 0.8391 (mttt) cc_final: 0.7921 (mmtt) REVERT: K 3846 LYS cc_start: 0.6593 (mtmt) cc_final: 0.5902 (tmtt) REVERT: K 3873 LYS cc_start: 0.8053 (ptmt) cc_final: 0.7661 (ptpp) REVERT: K 3876 ASP cc_start: 0.8389 (m-30) cc_final: 0.7647 (p0) REVERT: K 3938 GLU cc_start: 0.7961 (tt0) cc_final: 0.7594 (tm-30) REVERT: N 28 LEU cc_start: 0.8912 (tp) cc_final: 0.8626 (mp) REVERT: N 51 TRP cc_start: 0.4981 (t60) cc_final: 0.3741 (t60) REVERT: N 226 ASP cc_start: 0.8308 (t0) cc_final: 0.7762 (t0) REVERT: N 320 ILE cc_start: 0.9114 (mp) cc_final: 0.8729 (pt) REVERT: T 468 TYR cc_start: 0.3352 (m-80) cc_final: 0.3094 (m-80) REVERT: T 503 MET cc_start: 0.6413 (mmm) cc_final: 0.5841 (mpp) REVERT: R 72 TRP cc_start: 0.6710 (m100) cc_final: 0.5153 (m100) outliers start: 52 outliers final: 32 residues processed: 383 average time/residue: 0.3507 time to fit residues: 197.8350 Evaluate side-chains 299 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 220 ARG Chi-restraints excluded: chain N residue 233 CYS Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 165 optimal weight: 40.0000 chunk 125 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 84 GLN C 94 ASN D 79 HIS E 55 GLN E 113 HIS ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 250 ASN N 273 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.136308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.100660 restraints weight = 53790.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100202 restraints weight = 33320.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.100899 restraints weight = 25222.375| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 21720 Z= 0.264 Angle : 0.721 10.659 30585 Z= 0.399 Chirality : 0.044 0.203 3438 Planarity : 0.005 0.084 2870 Dihedral : 27.614 178.534 5203 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 4.89 % Allowed : 13.10 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.18), residues: 1830 helix: 0.86 (0.21), residues: 577 sheet: -2.50 (0.28), residues: 271 loop : -2.91 (0.17), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 59 HIS 0.009 0.002 HIS B 75 PHE 0.024 0.002 PHE K3885 TYR 0.028 0.002 TYR N 13 ARG 0.005 0.001 ARG N 190 Details of bonding type rmsd hydrogen bonds : bond 0.06449 ( 898) hydrogen bonds : angle 4.33071 ( 2250) metal coordination : bond 0.00168 ( 2) covalent geometry : bond 0.00597 (21716) covalent geometry : angle 0.72062 (30585) Misc. bond : bond 0.00170 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 282 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.7709 (mt0) cc_final: 0.7498 (mm110) REVERT: B 44 LYS cc_start: 0.8413 (mtpt) cc_final: 0.7972 (mtmt) REVERT: B 63 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8186 (mm-30) REVERT: C 73 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8545 (t0) REVERT: D 30 ARG cc_start: 0.7425 (mtp180) cc_final: 0.7194 (mtp85) REVERT: D 48 ASP cc_start: 0.6606 (t0) cc_final: 0.6282 (t0) REVERT: D 54 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8783 (mmmm) REVERT: F 25 ASN cc_start: 0.8417 (t0) cc_final: 0.8058 (t0) REVERT: F 88 TYR cc_start: 0.8706 (m-10) cc_final: 0.8438 (m-10) REVERT: G 92 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7610 (mm-30) REVERT: H 30 ARG cc_start: 0.8278 (mpt180) cc_final: 0.7492 (mmp80) REVERT: H 40 LYS cc_start: 0.9129 (mptt) cc_final: 0.8926 (mptt) REVERT: H 82 LYS cc_start: 0.8410 (mttt) cc_final: 0.7941 (mmtt) REVERT: K 3898 HIS cc_start: 0.8256 (m-70) cc_final: 0.7321 (m-70) REVERT: K 3938 GLU cc_start: 0.7659 (tt0) cc_final: 0.7248 (tm-30) REVERT: N 320 ILE cc_start: 0.9238 (mp) cc_final: 0.8876 (pt) REVERT: N 373 GLU cc_start: 0.7162 (mp0) cc_final: 0.6956 (mp0) REVERT: T 500 MET cc_start: -0.0611 (ptm) cc_final: -0.1535 (ptm) REVERT: T 503 MET cc_start: 0.6451 (mmm) cc_final: 0.5515 (mpp) REVERT: R 72 TRP cc_start: 0.6704 (m100) cc_final: 0.5832 (m100) REVERT: R 284 TYR cc_start: 0.1169 (m-10) cc_final: 0.0923 (m-80) outliers start: 78 outliers final: 54 residues processed: 331 average time/residue: 0.3292 time to fit residues: 164.9269 Evaluate side-chains 304 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 249 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3848 ASN Chi-restraints excluded: chain K residue 3863 ILE Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 128 MET Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 220 ARG Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 307 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 53 optimal weight: 0.0570 chunk 75 optimal weight: 8.9990 chunk 180 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 169 optimal weight: 30.0000 chunk 4 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 94 ASN D 106 HIS ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 250 ASN N 273 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 354 GLN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.141754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.107237 restraints weight = 54343.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.107674 restraints weight = 34618.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.108194 restraints weight = 26173.003| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21720 Z= 0.137 Angle : 0.593 7.937 30585 Z= 0.335 Chirality : 0.040 0.211 3438 Planarity : 0.004 0.068 2870 Dihedral : 27.341 176.075 5203 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.26 % Allowed : 14.92 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.19), residues: 1830 helix: 1.67 (0.21), residues: 582 sheet: -2.28 (0.28), residues: 290 loop : -2.72 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 156 HIS 0.008 0.001 HIS R 44 PHE 0.016 0.001 PHE N 189 TYR 0.019 0.001 TYR H 37 ARG 0.003 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 898) hydrogen bonds : angle 3.51604 ( 2250) metal coordination : bond 0.00109 ( 2) covalent geometry : bond 0.00296 (21716) covalent geometry : angle 0.59256 (30585) Misc. bond : bond 0.00150 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 303 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8696 (m) cc_final: 0.8449 (p) REVERT: C 56 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6894 (tp30) REVERT: C 84 GLN cc_start: 0.9558 (tp-100) cc_final: 0.9110 (tp40) REVERT: C 94 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8694 (t0) REVERT: F 88 TYR cc_start: 0.8564 (m-10) cc_final: 0.7595 (m-10) REVERT: G 18 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.7985 (p) REVERT: H 82 LYS cc_start: 0.8219 (mttt) cc_final: 0.7834 (mmtt) REVERT: K 3876 ASP cc_start: 0.8628 (m-30) cc_final: 0.7928 (p0) REVERT: K 3938 GLU cc_start: 0.7705 (tt0) cc_final: 0.7241 (tm-30) REVERT: N 220 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7424 (ptp-110) REVERT: N 320 ILE cc_start: 0.9180 (mp) cc_final: 0.8871 (pt) REVERT: N 339 LEU cc_start: 0.8557 (pp) cc_final: 0.8281 (pp) REVERT: N 340 ASP cc_start: 0.8644 (t0) cc_final: 0.8346 (t0) REVERT: T 500 MET cc_start: -0.0173 (ptm) cc_final: -0.1023 (ptm) REVERT: T 503 MET cc_start: 0.6450 (mmm) cc_final: 0.5501 (mpp) REVERT: R 72 TRP cc_start: 0.6572 (m100) cc_final: 0.5539 (m100) REVERT: R 140 GLN cc_start: 0.4654 (mt0) cc_final: 0.4322 (mm110) REVERT: R 228 TYR cc_start: 0.7365 (m-80) cc_final: 0.6962 (m-80) REVERT: R 284 TYR cc_start: 0.1234 (m-10) cc_final: 0.0869 (m-80) outliers start: 52 outliers final: 31 residues processed: 337 average time/residue: 0.3405 time to fit residues: 174.5313 Evaluate side-chains 300 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 265 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 128 MET Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 220 ARG Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 384 SER Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 94 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN F 75 HIS ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.136632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.097344 restraints weight = 54106.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.097769 restraints weight = 35200.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098648 restraints weight = 27882.752| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 21720 Z= 0.245 Angle : 0.694 11.455 30585 Z= 0.382 Chirality : 0.043 0.208 3438 Planarity : 0.004 0.080 2870 Dihedral : 27.583 178.250 5203 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 4.95 % Allowed : 15.11 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.19), residues: 1830 helix: 1.21 (0.21), residues: 577 sheet: -2.20 (0.28), residues: 293 loop : -2.67 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 156 HIS 0.009 0.002 HIS K3898 PHE 0.017 0.002 PHE K3885 TYR 0.027 0.002 TYR N 13 ARG 0.009 0.001 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.06207 ( 898) hydrogen bonds : angle 4.05715 ( 2250) metal coordination : bond 0.00129 ( 2) covalent geometry : bond 0.00553 (21716) covalent geometry : angle 0.69411 (30585) Misc. bond : bond 0.00169 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 263 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8777 (m) cc_final: 0.8520 (p) REVERT: B 31 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8169 (tptp) REVERT: B 63 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8196 (mm-30) REVERT: C 56 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6880 (tp30) REVERT: C 94 ASN cc_start: 0.9279 (OUTLIER) cc_final: 0.8837 (t0) REVERT: D 48 ASP cc_start: 0.6920 (t0) cc_final: 0.6548 (t0) REVERT: D 54 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8782 (mmmm) REVERT: F 88 TYR cc_start: 0.8613 (m-10) cc_final: 0.7734 (m-10) REVERT: G 18 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8076 (p) REVERT: G 84 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: H 30 ARG cc_start: 0.8400 (mpt180) cc_final: 0.7615 (mmp80) REVERT: H 80 TYR cc_start: 0.7337 (m-10) cc_final: 0.6590 (m-80) REVERT: H 82 LYS cc_start: 0.8416 (mttt) cc_final: 0.8178 (mttm) REVERT: K 3845 CYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7494 (m) REVERT: K 3876 ASP cc_start: 0.8860 (m-30) cc_final: 0.8114 (p0) REVERT: K 3938 GLU cc_start: 0.7315 (tt0) cc_final: 0.6845 (tm-30) REVERT: K 3940 LEU cc_start: 0.8830 (mm) cc_final: 0.8267 (mm) REVERT: N 220 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7609 (ptp-110) REVERT: N 226 ASP cc_start: 0.8549 (t0) cc_final: 0.7774 (t0) REVERT: N 320 ILE cc_start: 0.9347 (mp) cc_final: 0.8990 (pt) REVERT: T 500 MET cc_start: -0.0263 (ptm) cc_final: -0.1542 (ptm) REVERT: T 503 MET cc_start: 0.6410 (mmm) cc_final: 0.5419 (mpp) REVERT: R 72 TRP cc_start: 0.6963 (m100) cc_final: 0.5729 (m100) REVERT: R 140 GLN cc_start: 0.4756 (mt0) cc_final: 0.4240 (mm110) REVERT: R 228 TYR cc_start: 0.7782 (m-80) cc_final: 0.7330 (m-80) REVERT: R 284 TYR cc_start: 0.1389 (m-10) cc_final: 0.1124 (m-80) outliers start: 79 outliers final: 55 residues processed: 314 average time/residue: 0.3525 time to fit residues: 170.2746 Evaluate side-chains 308 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 246 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3863 ILE Chi-restraints excluded: chain K residue 3872 GLU Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 128 MET Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 220 ARG Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 43 optimal weight: 0.8980 chunk 168 optimal weight: 20.0000 chunk 206 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 59 optimal weight: 0.0170 chunk 30 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 overall best weight: 2.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.137645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.099471 restraints weight = 53142.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.099867 restraints weight = 37465.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.100422 restraints weight = 24299.690| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21720 Z= 0.197 Angle : 0.648 9.932 30585 Z= 0.360 Chirality : 0.041 0.210 3438 Planarity : 0.004 0.076 2870 Dihedral : 27.508 176.881 5203 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 4.33 % Allowed : 16.49 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.19), residues: 1830 helix: 1.31 (0.21), residues: 578 sheet: -2.13 (0.28), residues: 306 loop : -2.62 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 156 HIS 0.009 0.001 HIS K3898 PHE 0.013 0.001 PHE K3885 TYR 0.020 0.002 TYR N 13 ARG 0.007 0.000 ARG N 294 Details of bonding type rmsd hydrogen bonds : bond 0.05291 ( 898) hydrogen bonds : angle 3.84635 ( 2250) metal coordination : bond 0.00124 ( 2) covalent geometry : bond 0.00444 (21716) covalent geometry : angle 0.64821 (30585) Misc. bond : bond 0.00183 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 263 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8842 (m) cc_final: 0.8626 (p) REVERT: C 94 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8835 (t0) REVERT: D 48 ASP cc_start: 0.6815 (t0) cc_final: 0.6467 (t0) REVERT: F 84 MET cc_start: 0.7359 (tpp) cc_final: 0.6843 (tpp) REVERT: F 88 TYR cc_start: 0.8600 (m-10) cc_final: 0.7780 (m-10) REVERT: G 18 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8094 (p) REVERT: G 84 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: G 104 GLN cc_start: 0.8699 (mp10) cc_final: 0.8239 (mp10) REVERT: H 30 ARG cc_start: 0.8366 (mpt180) cc_final: 0.7607 (mmp80) REVERT: H 80 TYR cc_start: 0.7374 (m-10) cc_final: 0.7050 (m-80) REVERT: H 82 LYS cc_start: 0.8361 (mttt) cc_final: 0.8101 (mttm) REVERT: K 3845 CYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7766 (m) REVERT: K 3876 ASP cc_start: 0.8883 (m-30) cc_final: 0.8139 (p0) REVERT: K 3906 ASN cc_start: 0.6677 (m-40) cc_final: 0.6297 (m110) REVERT: K 3938 GLU cc_start: 0.7336 (tt0) cc_final: 0.6747 (tm-30) REVERT: N 220 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7589 (ptp-110) REVERT: N 226 ASP cc_start: 0.8526 (t0) cc_final: 0.7732 (t0) REVERT: N 320 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.8995 (pt) REVERT: N 339 LEU cc_start: 0.8354 (pp) cc_final: 0.8112 (pp) REVERT: T 336 MET cc_start: 0.3453 (mmm) cc_final: 0.2684 (mmm) REVERT: T 500 MET cc_start: -0.0285 (ptm) cc_final: -0.1480 (ptm) REVERT: T 503 MET cc_start: 0.6451 (mmm) cc_final: 0.5706 (mpp) REVERT: R 44 HIS cc_start: 0.4808 (m-70) cc_final: 0.4371 (t-90) REVERT: R 53 PHE cc_start: 0.5163 (OUTLIER) cc_final: 0.3669 (m-80) REVERT: R 72 TRP cc_start: 0.6814 (m100) cc_final: 0.5521 (m100) REVERT: R 140 GLN cc_start: 0.5229 (mt0) cc_final: 0.4709 (mm110) outliers start: 69 outliers final: 52 residues processed: 311 average time/residue: 0.3302 time to fit residues: 157.3812 Evaluate side-chains 308 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 249 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3872 GLU Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3898 HIS Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 128 MET Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 220 ARG Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 309 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 199 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 354 GLN ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.140649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.106635 restraints weight = 53766.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.107064 restraints weight = 35198.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.107625 restraints weight = 28827.940| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21720 Z= 0.140 Angle : 0.600 10.999 30585 Z= 0.333 Chirality : 0.039 0.205 3438 Planarity : 0.004 0.071 2870 Dihedral : 27.288 176.134 5203 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.70 % Allowed : 17.12 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.20), residues: 1830 helix: 1.74 (0.22), residues: 582 sheet: -2.00 (0.28), residues: 323 loop : -2.53 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 35 HIS 0.008 0.001 HIS K3898 PHE 0.015 0.001 PHE N 189 TYR 0.019 0.001 TYR H 37 ARG 0.004 0.000 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 898) hydrogen bonds : angle 3.40900 ( 2250) metal coordination : bond 0.00041 ( 2) covalent geometry : bond 0.00304 (21716) covalent geometry : angle 0.60037 (30585) Misc. bond : bond 0.00144 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 287 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6837 (tp30) REVERT: C 68 ASN cc_start: 0.8736 (t0) cc_final: 0.8506 (t0) REVERT: C 94 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8832 (t0) REVERT: D 48 ASP cc_start: 0.6587 (t0) cc_final: 0.6265 (t0) REVERT: D 54 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8614 (mmmm) REVERT: G 104 GLN cc_start: 0.8600 (mp10) cc_final: 0.8079 (mp10) REVERT: H 30 ARG cc_start: 0.8417 (mpt180) cc_final: 0.7613 (mmp80) REVERT: H 76 ARG cc_start: 0.8335 (ttp-110) cc_final: 0.8066 (ttm170) REVERT: H 82 LYS cc_start: 0.8185 (mttt) cc_final: 0.7874 (mmtt) REVERT: K 3845 CYS cc_start: 0.8708 (OUTLIER) cc_final: 0.7883 (m) REVERT: K 3876 ASP cc_start: 0.8679 (m-30) cc_final: 0.7987 (p0) REVERT: K 3931 MET cc_start: 0.7013 (tpp) cc_final: 0.6772 (tpt) REVERT: K 3938 GLU cc_start: 0.7716 (tt0) cc_final: 0.7127 (tm-30) REVERT: K 3940 LEU cc_start: 0.8666 (mm) cc_final: 0.8243 (mm) REVERT: N 226 ASP cc_start: 0.8445 (t0) cc_final: 0.7677 (t0) REVERT: N 320 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8850 (pt) REVERT: N 339 LEU cc_start: 0.8510 (pp) cc_final: 0.8242 (pp) REVERT: T 336 MET cc_start: 0.4474 (mmm) cc_final: 0.3738 (mmm) REVERT: T 500 MET cc_start: -0.0176 (ptm) cc_final: -0.1117 (ptm) REVERT: T 503 MET cc_start: 0.6233 (mmm) cc_final: 0.5736 (mpp) REVERT: R 44 HIS cc_start: 0.4405 (m-70) cc_final: 0.4185 (t-90) REVERT: R 53 PHE cc_start: 0.4788 (OUTLIER) cc_final: 0.3243 (m-80) REVERT: R 72 TRP cc_start: 0.6474 (m100) cc_final: 0.5196 (m100) REVERT: R 140 GLN cc_start: 0.5486 (mt0) cc_final: 0.5134 (mm110) outliers start: 59 outliers final: 45 residues processed: 325 average time/residue: 0.3400 time to fit residues: 167.5029 Evaluate side-chains 319 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3816 MET Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3872 GLU Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3898 HIS Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain K residue 3946 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 128 MET Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 316 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 180 optimal weight: 0.0980 chunk 152 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 71 optimal weight: 0.0570 chunk 170 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 189 optimal weight: 30.0000 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 456 GLN ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.140582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.106421 restraints weight = 53945.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.107502 restraints weight = 32808.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.108015 restraints weight = 25338.361| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21720 Z= 0.146 Angle : 0.608 10.789 30585 Z= 0.337 Chirality : 0.040 0.299 3438 Planarity : 0.004 0.076 2870 Dihedral : 27.257 176.870 5203 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.57 % Allowed : 17.93 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.20), residues: 1830 helix: 1.89 (0.22), residues: 575 sheet: -1.96 (0.28), residues: 321 loop : -2.48 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 35 HIS 0.008 0.001 HIS K3898 PHE 0.015 0.001 PHE N 189 TYR 0.019 0.001 TYR H 37 ARG 0.004 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 898) hydrogen bonds : angle 3.39621 ( 2250) metal coordination : bond 0.00062 ( 2) covalent geometry : bond 0.00325 (21716) covalent geometry : angle 0.60823 (30585) Misc. bond : bond 0.00159 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.7781 (tpt) cc_final: 0.7520 (tpt) REVERT: C 56 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: C 68 ASN cc_start: 0.8719 (t0) cc_final: 0.8506 (t0) REVERT: C 94 ASN cc_start: 0.9247 (OUTLIER) cc_final: 0.8759 (t0) REVERT: D 48 ASP cc_start: 0.6623 (t0) cc_final: 0.6288 (t0) REVERT: F 84 MET cc_start: 0.7390 (tpp) cc_final: 0.6813 (tpp) REVERT: F 88 TYR cc_start: 0.8545 (m-10) cc_final: 0.7667 (m-10) REVERT: G 18 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8073 (p) REVERT: G 104 GLN cc_start: 0.8605 (mp10) cc_final: 0.7988 (mp10) REVERT: H 30 ARG cc_start: 0.8387 (mpt180) cc_final: 0.7791 (mmp80) REVERT: H 76 ARG cc_start: 0.8426 (ttp-110) cc_final: 0.8121 (ttm170) REVERT: H 80 TYR cc_start: 0.7166 (m-10) cc_final: 0.6903 (m-80) REVERT: H 82 LYS cc_start: 0.8162 (mttt) cc_final: 0.7815 (mmtt) REVERT: K 3845 CYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7871 (m) REVERT: K 3876 ASP cc_start: 0.8728 (m-30) cc_final: 0.8050 (p0) REVERT: K 3938 GLU cc_start: 0.7552 (tt0) cc_final: 0.7069 (tm-30) REVERT: K 3940 LEU cc_start: 0.8602 (mm) cc_final: 0.8292 (mm) REVERT: N 226 ASP cc_start: 0.8455 (t0) cc_final: 0.7716 (t0) REVERT: N 256 LYS cc_start: 0.8703 (tppt) cc_final: 0.8417 (tppt) REVERT: N 320 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8882 (pt) REVERT: N 339 LEU cc_start: 0.8477 (pp) cc_final: 0.8186 (pp) REVERT: T 336 MET cc_start: 0.4399 (mmm) cc_final: 0.3714 (mmm) REVERT: T 346 TRP cc_start: 0.1816 (m100) cc_final: 0.1566 (m100) REVERT: T 500 MET cc_start: -0.0224 (ptm) cc_final: -0.1171 (ptm) REVERT: T 503 MET cc_start: 0.6185 (mmm) cc_final: 0.5714 (mpp) REVERT: R 53 PHE cc_start: 0.4859 (OUTLIER) cc_final: 0.3377 (m-80) REVERT: R 72 TRP cc_start: 0.6509 (m100) cc_final: 0.5214 (m100) REVERT: R 140 GLN cc_start: 0.5489 (mt0) cc_final: 0.5209 (mm110) outliers start: 57 outliers final: 45 residues processed: 312 average time/residue: 0.3239 time to fit residues: 156.4991 Evaluate side-chains 315 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain K residue 3872 GLU Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain K residue 3946 PHE Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 128 MET Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 316 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 85 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 177 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 164 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.137805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.099795 restraints weight = 53270.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.100077 restraints weight = 37843.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100344 restraints weight = 25536.522| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21720 Z= 0.206 Angle : 0.656 12.219 30585 Z= 0.362 Chirality : 0.042 0.205 3438 Planarity : 0.004 0.081 2870 Dihedral : 27.378 177.743 5203 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.82 % Allowed : 18.12 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.19), residues: 1830 helix: 1.54 (0.21), residues: 575 sheet: -1.97 (0.28), residues: 319 loop : -2.49 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 35 HIS 0.011 0.001 HIS K3898 PHE 0.013 0.001 PHE K3885 TYR 0.022 0.002 TYR N 13 ARG 0.004 0.000 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.05454 ( 898) hydrogen bonds : angle 3.76704 ( 2250) metal coordination : bond 0.00108 ( 2) covalent geometry : bond 0.00467 (21716) covalent geometry : angle 0.65562 (30585) Misc. bond : bond 0.00167 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 264 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6898 (tp30) REVERT: C 94 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8752 (t0) REVERT: D 48 ASP cc_start: 0.6774 (t0) cc_final: 0.6415 (t0) REVERT: E 63 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7668 (tpp-160) REVERT: F 84 MET cc_start: 0.7475 (tpp) cc_final: 0.7025 (tpp) REVERT: F 88 TYR cc_start: 0.8688 (m-10) cc_final: 0.7692 (m-10) REVERT: G 18 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8101 (p) REVERT: H 30 ARG cc_start: 0.8391 (mpt180) cc_final: 0.7792 (mmp80) REVERT: H 80 TYR cc_start: 0.7391 (m-10) cc_final: 0.6970 (m-80) REVERT: H 82 LYS cc_start: 0.8322 (mttt) cc_final: 0.8069 (mttm) REVERT: K 3828 LYS cc_start: 0.7832 (pttm) cc_final: 0.7501 (pttm) REVERT: K 3845 CYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7490 (m) REVERT: K 3876 ASP cc_start: 0.8842 (m-30) cc_final: 0.8103 (p0) REVERT: K 3938 GLU cc_start: 0.7212 (tt0) cc_final: 0.6768 (tm-30) REVERT: N 256 LYS cc_start: 0.8635 (tppt) cc_final: 0.8368 (tppt) REVERT: N 320 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8977 (pt) REVERT: N 339 LEU cc_start: 0.8377 (pp) cc_final: 0.8119 (pp) REVERT: T 500 MET cc_start: -0.0404 (ptm) cc_final: -0.1570 (ptm) REVERT: T 503 MET cc_start: 0.6186 (mmm) cc_final: 0.5601 (mpp) REVERT: R 72 TRP cc_start: 0.6636 (m100) cc_final: 0.5467 (m100) REVERT: R 140 GLN cc_start: 0.5543 (mt0) cc_final: 0.5162 (mm110) REVERT: R 221 LYS cc_start: 0.8199 (ptmm) cc_final: 0.7946 (ptmm) outliers start: 61 outliers final: 45 residues processed: 309 average time/residue: 0.3204 time to fit residues: 152.3379 Evaluate side-chains 306 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain K residue 3872 GLU Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3946 PHE Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 128 MET Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 316 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Chi-restraints excluded: chain R residue 301 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 54 optimal weight: 10.0000 chunk 204 optimal weight: 20.0000 chunk 123 optimal weight: 0.0970 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3906 ASN ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.142005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.108318 restraints weight = 54027.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.108612 restraints weight = 35138.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.109364 restraints weight = 27921.628| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21720 Z= 0.134 Angle : 0.616 10.585 30585 Z= 0.339 Chirality : 0.040 0.184 3438 Planarity : 0.004 0.072 2870 Dihedral : 27.102 176.016 5203 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.88 % Allowed : 19.18 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.20), residues: 1830 helix: 1.86 (0.22), residues: 581 sheet: -1.88 (0.27), residues: 324 loop : -2.44 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 35 HIS 0.009 0.001 HIS K3898 PHE 0.016 0.001 PHE N 189 TYR 0.020 0.001 TYR H 37 ARG 0.008 0.000 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 898) hydrogen bonds : angle 3.32835 ( 2250) metal coordination : bond 0.00081 ( 2) covalent geometry : bond 0.00291 (21716) covalent geometry : angle 0.61612 (30585) Misc. bond : bond 0.00165 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 290 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: D 48 ASP cc_start: 0.6504 (t0) cc_final: 0.6207 (t0) REVERT: E 133 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7375 (tt0) REVERT: G 92 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7119 (mm-30) REVERT: G 104 GLN cc_start: 0.8523 (mp10) cc_final: 0.7902 (mp10) REVERT: H 30 ARG cc_start: 0.8455 (mpt180) cc_final: 0.7664 (mmp80) REVERT: H 76 ARG cc_start: 0.8324 (ttp-110) cc_final: 0.8043 (ttm170) REVERT: H 82 LYS cc_start: 0.8148 (mttt) cc_final: 0.7830 (mmtt) REVERT: K 3828 LYS cc_start: 0.7770 (pttm) cc_final: 0.7399 (pttm) REVERT: K 3845 CYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7758 (m) REVERT: K 3872 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8976 (mp0) REVERT: K 3876 ASP cc_start: 0.8748 (m-30) cc_final: 0.7988 (p0) REVERT: K 3931 MET cc_start: 0.6929 (tpp) cc_final: 0.6487 (tpt) REVERT: K 3938 GLU cc_start: 0.7333 (tt0) cc_final: 0.7121 (tm-30) REVERT: N 226 ASP cc_start: 0.8371 (t0) cc_final: 0.7560 (t0) REVERT: N 256 LYS cc_start: 0.8603 (tppt) cc_final: 0.8305 (tppt) REVERT: N 320 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8896 (pt) REVERT: N 339 LEU cc_start: 0.8423 (pp) cc_final: 0.8108 (pp) REVERT: T 336 MET cc_start: 0.4177 (mmm) cc_final: 0.3212 (mmm) REVERT: T 346 TRP cc_start: 0.1499 (m100) cc_final: 0.1204 (m100) REVERT: T 500 MET cc_start: -0.0229 (ptm) cc_final: -0.1270 (ptm) REVERT: T 503 MET cc_start: 0.6120 (mmm) cc_final: 0.5678 (mpp) REVERT: R 53 PHE cc_start: 0.4830 (OUTLIER) cc_final: 0.3329 (m-80) REVERT: R 72 TRP cc_start: 0.6260 (m100) cc_final: 0.5186 (m100) REVERT: R 221 LYS cc_start: 0.7739 (ptmm) cc_final: 0.7509 (ptmm) outliers start: 46 outliers final: 37 residues processed: 321 average time/residue: 0.3264 time to fit residues: 162.3262 Evaluate side-chains 305 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain K residue 3872 GLU Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3898 HIS Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain K residue 3946 PHE Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 90 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3839 HIS ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3906 ASN ** N 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.136022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098653 restraints weight = 54213.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098256 restraints weight = 40696.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.098938 restraints weight = 26795.632| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 21720 Z= 0.279 Angle : 0.738 12.954 30585 Z= 0.403 Chirality : 0.045 0.236 3438 Planarity : 0.005 0.086 2870 Dihedral : 27.491 178.436 5203 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 3.39 % Allowed : 19.00 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.19), residues: 1830 helix: 1.21 (0.21), residues: 575 sheet: -1.87 (0.28), residues: 301 loop : -2.57 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 35 HIS 0.010 0.002 HIS K3898 PHE 0.019 0.002 PHE K3885 TYR 0.026 0.002 TYR N 13 ARG 0.009 0.001 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.06441 ( 898) hydrogen bonds : angle 4.13010 ( 2250) metal coordination : bond 0.00154 ( 2) covalent geometry : bond 0.00636 (21716) covalent geometry : angle 0.73787 (30585) Misc. bond : bond 0.00183 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6496.65 seconds wall clock time: 114 minutes 27.84 seconds (6867.84 seconds total)