Starting phenix.real_space_refine on Mon Sep 14 02:19:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kiv_9999/09_2026/6kiv_9999.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kiv_9999/09_2026/6kiv_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_9999/09_2026/6kiv_9999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kiv_9999/09_2026/6kiv_9999.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6kiv_9999/09_2026/6kiv_9999.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kiv_9999/09_2026/6kiv_9999.cif" model { file = "/net/cci-nas-00/data/ceres_data/6kiv_9999/09_2026/6kiv_9999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kiv_9999/09_2026/6kiv_9999.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'HIS:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU: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: 4.26, per 1000 atoms: 0.21 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: 1.63 Conformation dependent library (CDL) restraints added in 717.0 milliseconds 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: 2.69 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: 4.80 Time building geometry restraints manager: 2.16 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=" N7 DA I 113 " pdb=" C5 DA I 113 " ideal model delta sigma weight residual 1.388 1.361 0.027 6.00e-03 2.78e+04 2.08e+01 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.435 1.491 -0.056 1.30e-02 5.92e+03 1.85e+01 bond pdb=" N1 DC I 82 " pdb=" C6 DC I 82 " ideal model delta sigma weight residual 1.367 1.343 0.024 6.00e-03 2.78e+04 1.63e+01 bond pdb=" C1' DC I 3 " pdb=" N1 DC I 3 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.39e+01 bond pdb=" C3' DG I 122 " pdb=" O3' DG I 122 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.20e+01 ... (remaining 21711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 29716 2.52 - 5.04: 806 5.04 - 7.55: 48 7.55 - 10.07: 13 10.07 - 12.59: 2 Bond angle restraints: 30585 Sorted by residual: angle pdb=" O4' DT I 48 " pdb=" C4' DT I 48 " pdb=" C3' DT I 48 " ideal model delta sigma weight residual 106.00 102.21 3.79 6.00e-01 2.78e+00 4.00e+01 angle pdb=" O4' DA I 49 " pdb=" C4' DA I 49 " pdb=" C3' DA I 49 " ideal model delta sigma weight residual 106.00 102.28 3.72 6.00e-01 2.78e+00 3.85e+01 angle pdb=" O4' DC I 54 " pdb=" C4' DC I 54 " pdb=" C3' DC I 54 " ideal model delta sigma weight residual 106.00 102.69 3.31 6.00e-01 2.78e+00 3.05e+01 angle pdb=" O4' DA I 20 " pdb=" C4' DA I 20 " pdb=" C3' DA I 20 " ideal model delta sigma weight residual 106.00 102.75 3.25 6.00e-01 2.78e+00 2.93e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 119.70 125.89 -6.19 1.20e+00 6.94e-01 2.66e+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 - 0.048: 2211 0.048 - 0.097: 909 0.097 - 0.145: 273 0.145 - 0.194: 37 0.194 - 0.242: 8 Chirality restraints: 3438 Sorted by residual: chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.46e+00 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 ... (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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.000 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 21720 Z= 0.593 Angle : 0.984 12.590 30585 Z= 0.726 Chirality : 0.056 0.242 3438 Planarity : 0.007 0.108 2870 Dihedral : 22.703 179.114 8794 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.16 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.009 0.001 ARG F 39 TYR 0.031 0.003 TYR B 51 PHE 0.023 0.003 PHE N 189 TRP 0.025 0.003 TRP N 303 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.59 (21716) covalent geometry : angle 0.98436 / 0.73 (30585) hydrogen bonds : bond 0.15019 / 10.04 ( 898) hydrogen bonds : angle 6.04261 / 4.24 ( 2250) metal coordination : bond 0.21670 / 15.09 ( 2) Misc. bond : bond 0.00378 / 0.25 ( 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 : 0.655 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: 0.8949 (p) REVERT: A 123 ASP cc_start: 0.8318 (m-30) cc_final: 0.8100 (m-30) REVERT: B 35 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8088 (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: 0.7614 (tmt-80) REVERT: D 54 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8810 (mmmm) REVERT: D 65 ASP cc_start: 0.8143 (t0) cc_final: 0.7874 (t0) REVERT: D 81 ASN cc_start: 0.8438 (m-40) cc_final: 0.8147 (m110) REVERT: D 88 SER cc_start: 0.9070 (p) cc_final: 0.8860 (p) REVERT: F 88 TYR cc_start: 0.8891 (m-10) cc_final: 0.7804 (m-10) REVERT: G 18 SER cc_start: 0.8315 (m) cc_final: 0.7611 (p) REVERT: G 61 GLU cc_start: 0.8672 (tp30) cc_final: 0.8329 (tm-30) REVERT: H 36 ILE cc_start: 0.8178 (pt) cc_final: 0.7941 (mp) REVERT: H 73 GLU cc_start: 0.8267 (tp30) cc_final: 0.8042 (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: 0.8109 (mmtt) REVERT: K 3828 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8217 (pttt) REVERT: K 3846 LYS cc_start: 0.6392 (mtmt) cc_final: 0.6075 (tmtt) REVERT: N 60 LYS cc_start: 0.8170 (tptt) cc_final: 0.7548 (tppt) REVERT: N 115 TYR cc_start: 0.5656 (m-80) cc_final: 0.5124 (m-10) REVERT: N 226 ASP cc_start: 0.7903 (t0) cc_final: 0.7654 (t0) REVERT: N 320 ILE cc_start: 0.8932 (mp) cc_final: 0.8639 (pt) REVERT: T 503 MET cc_start: 0.6152 (mmm) cc_final: 0.5485 (mtm) REVERT: R 72 TRP cc_start: 0.6754 (m100) cc_final: 0.5445 (m100) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.2055 time to fit residues: 148.5618 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 : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0470 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 overall best weight: 2.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS C 38 ASN C 84 GLN C 94 ASN D 79 HIS D 81 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN G 110 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 HIS N 328 ASN ** O 41 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 = 0.4177 r_free = 0.4177 target = 0.139081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.102800 restraints weight = 53330.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102473 restraints weight = 31769.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.103162 restraints weight = 22888.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103505 restraints weight = 21402.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.103564 restraints weight = 18754.777| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21720 Z= 0.206 Angle : 0.782 13.936 30585 Z= 0.435 Chirality : 0.053 0.362 3438 Planarity : 0.006 0.107 2870 Dihedral : 28.127 178.631 5203 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.31 % Favored : 91.64 % Rotamer: Outliers : 2.57 % Allowed : 12.41 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.18), residues: 1830 helix: 0.40 (0.21), residues: 563 sheet: -2.59 (0.27), residues: 298 loop : -3.01 (0.17), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 105 TYR 0.044 0.002 TYR B 51 PHE 0.020 0.002 PHE R 222 TRP 0.027 0.002 TRP R 156 HIS 0.014 0.002 HIS R 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (21716) covalent geometry : angle 0.78235 / 0.43 (30585) hydrogen bonds : bond 0.06916 / 4.55 ( 898) hydrogen bonds : angle 4.63415 / 3.29 ( 2250) metal coordination : bond 0.00606 / 0.43 ( 2) Misc. bond : bond 0.00183 / 0.13 ( 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 368 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 327 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 LEU cc_start: 0.8910 (tp) cc_final: 0.8697 (tt) REVERT: C 73 ASN cc_start: 0.8855 (t0) cc_final: 0.8555 (t0) REVERT: C 94 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.8968 (t0) REVERT: D 27 ARG cc_start: 0.7673 (tmt170) cc_final: 0.7422 (tmt-80) REVERT: D 44 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8050 (tm-30) REVERT: D 81 ASN cc_start: 0.8537 (m110) cc_final: 0.8311 (m110) REVERT: E 73 GLU cc_start: 0.8045 (tt0) cc_final: 0.7799 (tt0) REVERT: F 25 ASN cc_start: 0.7930 (t0) cc_final: 0.7692 (t0) REVERT: F 88 TYR cc_start: 0.8755 (m-10) cc_final: 0.8471 (m-10) REVERT: H 36 ILE cc_start: 0.8189 (pt) cc_final: 0.7979 (pt) REVERT: H 82 LYS cc_start: 0.8521 (mttt) cc_final: 0.8028 (mmtt) REVERT: K 3857 GLU cc_start: 0.7990 (tt0) cc_final: 0.7679 (tt0) REVERT: K 3889 ASP cc_start: 0.5786 (p0) cc_final: 0.5562 (m-30) REVERT: K 3894 ASP cc_start: 0.8593 (t0) cc_final: 0.8039 (t0) REVERT: K 3938 GLU cc_start: 0.7881 (tt0) cc_final: 0.7456 (tm-30) REVERT: K 3940 LEU cc_start: 0.8594 (mm) cc_final: 0.8167 (mm) REVERT: N 12 ASN cc_start: 0.4352 (t0) cc_final: 0.4095 (t0) REVERT: N 51 TRP cc_start: 0.5106 (t60) cc_final: 0.3759 (t60) REVERT: N 65 HIS cc_start: 0.6984 (OUTLIER) cc_final: 0.6757 (t-90) REVERT: N 226 ASP cc_start: 0.8441 (t0) cc_final: 0.7711 (t0) REVERT: N 320 ILE cc_start: 0.9201 (mp) cc_final: 0.8778 (pt) REVERT: T 336 MET cc_start: 0.4996 (mmm) cc_final: 0.4734 (mmm) REVERT: T 503 MET cc_start: 0.6261 (mmm) cc_final: 0.5629 (mpp) REVERT: R 72 TRP cc_start: 0.7172 (m100) cc_final: 0.5815 (m100) outliers start: 41 outliers final: 29 residues processed: 349 average time/residue: 0.1607 time to fit residues: 83.7235 Evaluate side-chains 296 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 63 ARG 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 23 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 3863 ILE Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 43 CYS Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 222 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 73 optimal weight: 40.0000 chunk 136 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN ** K3861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.140453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.105833 restraints weight = 53541.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106416 restraints weight = 34779.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.106865 restraints weight = 27540.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.106966 restraints weight = 22776.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107107 restraints weight = 21210.064| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21720 Z= 0.152 Angle : 0.682 12.340 30585 Z= 0.388 Chirality : 0.049 0.362 3438 Planarity : 0.005 0.096 2870 Dihedral : 27.985 179.707 5203 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.07 % Allowed : 13.54 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.19), residues: 1830 helix: 1.23 (0.22), residues: 566 sheet: -2.43 (0.27), residues: 311 loop : -2.93 (0.17), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 92 TYR 0.034 0.002 TYR B 51 PHE 0.020 0.001 PHE N 189 TRP 0.030 0.002 TRP R 59 HIS 0.009 0.001 HIS R 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (21716) covalent geometry : angle 0.68234 / 0.39 (30585) hydrogen bonds : bond 0.05649 / 3.70 ( 898) hydrogen bonds : angle 4.18533 / 2.96 ( 2250) metal coordination : bond 0.00093 / 0.06 ( 2) Misc. bond : bond 0.00145 / 0.10 ( 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 357 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 308 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7563 (mmt180) REVERT: A 73 GLU cc_start: 0.7097 (tt0) cc_final: 0.6863 (tt0) REVERT: B 92 ARG cc_start: 0.8549 (mtp-110) cc_final: 0.8233 (ttp-110) REVERT: D 27 ARG cc_start: 0.7815 (tmt170) cc_final: 0.7614 (tmt-80) REVERT: D 44 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8148 (tm-30) REVERT: D 54 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8436 (mmmm) REVERT: D 81 ASN cc_start: 0.8521 (m110) cc_final: 0.8246 (m110) REVERT: E 73 GLU cc_start: 0.7995 (tt0) cc_final: 0.7667 (tt0) REVERT: F 25 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7763 (t0) REVERT: F 88 TYR cc_start: 0.8677 (m-10) cc_final: 0.7327 (m-10) REVERT: F 92 ARG cc_start: 0.8510 (mtp-110) cc_final: 0.8310 (ttp80) REVERT: G 61 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7883 (tm-30) REVERT: H 80 TYR cc_start: 0.7331 (m-10) cc_final: 0.6304 (m-10) REVERT: H 82 LYS cc_start: 0.8501 (mttt) cc_final: 0.8052 (mmtt) REVERT: K 3846 LYS cc_start: 0.6641 (mtmt) cc_final: 0.5929 (tmtt) REVERT: K 3876 ASP cc_start: 0.8544 (m-30) cc_final: 0.7703 (p0) REVERT: K 3918 ILE cc_start: 0.7869 (pt) cc_final: 0.7332 (pt) REVERT: N 51 TRP cc_start: 0.4948 (t60) cc_final: 0.3740 (t60) REVERT: N 226 ASP cc_start: 0.8407 (t0) cc_final: 0.7696 (t0) REVERT: N 320 ILE cc_start: 0.9134 (mp) cc_final: 0.8772 (pt) REVERT: T 336 MET cc_start: 0.5514 (mmm) cc_final: 0.5292 (mmm) REVERT: T 500 MET cc_start: -0.0574 (ptm) cc_final: -0.1112 (ptm) REVERT: T 503 MET cc_start: 0.6274 (mmm) cc_final: 0.5707 (mpp) REVERT: R 72 TRP cc_start: 0.6767 (m100) cc_final: 0.5182 (m100) REVERT: R 284 TYR cc_start: 0.0917 (m-10) cc_final: 0.0495 (m-80) outliers start: 49 outliers final: 32 residues processed: 336 average time/residue: 0.1554 time to fit residues: 79.4019 Evaluate side-chains 301 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 63 ARG Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3863 ILE Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 81 LEU 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 257 CYS Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 222 PHE 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 195 optimal weight: 7.9990 chunk 149 optimal weight: 20.0000 chunk 170 optimal weight: 30.0000 chunk 199 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.139075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.101925 restraints weight = 53755.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101883 restraints weight = 37869.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102010 restraints weight = 26129.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.102438 restraints weight = 23525.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.102751 restraints weight = 20603.553| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21720 Z= 0.179 Angle : 0.694 11.952 30585 Z= 0.387 Chirality : 0.048 0.357 3438 Planarity : 0.005 0.085 2870 Dihedral : 27.918 179.531 5203 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.01 % Allowed : 14.48 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.19), residues: 1830 helix: 1.32 (0.21), residues: 571 sheet: -2.25 (0.28), residues: 299 loop : -2.91 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.039 0.002 TYR K3875 PHE 0.019 0.001 PHE K3885 TRP 0.034 0.002 TRP R 59 HIS 0.010 0.001 HIS K3898 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (21716) covalent geometry : angle 0.69361 / 0.39 (30585) hydrogen bonds : bond 0.05802 / 3.80 ( 898) hydrogen bonds : angle 4.15598 / 2.96 ( 2250) metal coordination : bond 0.00171 / 0.12 ( 2) Misc. bond : bond 0.00172 / 0.12 ( 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 348 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 284 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8852 (m) cc_final: 0.8449 (p) REVERT: B 92 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8277 (ttp-110) REVERT: C 94 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8957 (t0) REVERT: D 27 ARG cc_start: 0.7703 (tmt170) cc_final: 0.7475 (tmt-80) REVERT: D 81 ASN cc_start: 0.8527 (m110) cc_final: 0.8307 (m110) REVERT: F 84 MET cc_start: 0.7251 (tpp) cc_final: 0.7023 (tpp) REVERT: F 88 TYR cc_start: 0.8682 (m-10) cc_final: 0.7269 (m-10) REVERT: H 80 TYR cc_start: 0.7341 (m-10) cc_final: 0.6263 (m-10) REVERT: H 82 LYS cc_start: 0.8584 (mttt) cc_final: 0.8288 (mttm) REVERT: K 3846 LYS cc_start: 0.6530 (mtmt) cc_final: 0.5835 (tmtt) REVERT: K 3876 ASP cc_start: 0.8318 (m-30) cc_final: 0.7917 (p0) REVERT: K 3938 GLU cc_start: 0.7576 (tt0) cc_final: 0.7127 (tm-30) REVERT: N 51 TRP cc_start: 0.5042 (t60) cc_final: 0.3845 (t60) REVERT: N 226 ASP cc_start: 0.8403 (t0) cc_final: 0.7624 (t0) REVERT: N 320 ILE cc_start: 0.9241 (mp) cc_final: 0.8822 (pt) REVERT: T 500 MET cc_start: -0.0381 (ptm) cc_final: -0.1379 (ptm) REVERT: T 503 MET cc_start: 0.6386 (mmm) cc_final: 0.5447 (mpp) REVERT: R 72 TRP cc_start: 0.6945 (m100) cc_final: 0.6123 (m100) REVERT: R 228 TYR cc_start: 0.7617 (m-80) cc_final: 0.7146 (m-80) REVERT: R 284 TYR cc_start: 0.1123 (m-10) cc_final: 0.0678 (m-80) outliers start: 64 outliers final: 47 residues processed: 320 average time/residue: 0.1589 time to fit residues: 77.2894 Evaluate side-chains 311 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG 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 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 73 THR 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 68 GLU 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 3848 ASN Chi-restraints excluded: chain K residue 3863 ILE Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain N residue 48 ILE 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 125 VAL Chi-restraints excluded: chain N residue 128 MET Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 195 CYS 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 100 optimal weight: 30.0000 chunk 171 optimal weight: 30.0000 chunk 207 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 96 optimal weight: 40.0000 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 148 optimal weight: 0.0470 chunk 19 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN D 106 HIS E 55 GLN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 273 GLN ** 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** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.140486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.105522 restraints weight = 53786.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.106226 restraints weight = 31507.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106822 restraints weight = 23411.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106801 restraints weight = 20834.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.106980 restraints weight = 18856.748| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21720 Z= 0.139 Angle : 0.651 10.143 30585 Z= 0.368 Chirality : 0.047 0.367 3438 Planarity : 0.004 0.081 2870 Dihedral : 27.821 179.171 5203 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.26 % Allowed : 15.55 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.19), residues: 1830 helix: 1.58 (0.22), residues: 574 sheet: -2.15 (0.29), residues: 292 loop : -2.76 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 154 TYR 0.021 0.002 TYR N 115 PHE 0.018 0.001 PHE N 206 TRP 0.015 0.001 TRP R 59 HIS 0.011 0.001 HIS K3898 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (21716) covalent geometry : angle 0.65053 / 0.37 (30585) hydrogen bonds : bond 0.05144 / 3.35 ( 898) hydrogen bonds : angle 3.85395 / 2.73 ( 2250) metal coordination : bond 0.00116 / 0.08 ( 2) Misc. bond : bond 0.00152 / 0.10 ( 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 349 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8809 (m) cc_final: 0.8436 (p) REVERT: B 44 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7492 (mtmt) REVERT: D 46 HIS cc_start: 0.8365 (m-70) cc_final: 0.8005 (m170) REVERT: D 81 ASN cc_start: 0.8403 (m110) cc_final: 0.8177 (m110) REVERT: F 84 MET cc_start: 0.7187 (tpp) cc_final: 0.6942 (tpp) REVERT: F 88 TYR cc_start: 0.8687 (m-10) cc_final: 0.7569 (m-10) REVERT: G 92 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7235 (mm-30) REVERT: H 80 TYR cc_start: 0.7331 (m-10) cc_final: 0.6531 (m-10) REVERT: H 82 LYS cc_start: 0.8504 (mttt) cc_final: 0.8010 (mmtt) REVERT: K 3846 LYS cc_start: 0.6656 (mtmt) cc_final: 0.6376 (ptpt) REVERT: K 3857 GLU cc_start: 0.7536 (tt0) cc_final: 0.7308 (tp30) REVERT: K 3938 GLU cc_start: 0.7373 (tt0) cc_final: 0.7060 (tm-30) REVERT: N 51 TRP cc_start: 0.4933 (t60) cc_final: 0.3784 (t60) REVERT: N 226 ASP cc_start: 0.8300 (t0) cc_final: 0.7772 (t0) REVERT: N 320 ILE cc_start: 0.9159 (mp) cc_final: 0.8801 (pt) REVERT: N 340 ASP cc_start: 0.8819 (t0) cc_final: 0.8038 (t0) REVERT: T 315 MET cc_start: 0.5564 (mtm) cc_final: 0.5301 (mtp) REVERT: T 500 MET cc_start: 0.0099 (ptm) cc_final: -0.0699 (ptm) REVERT: T 503 MET cc_start: 0.6390 (mmm) cc_final: 0.5497 (mpp) REVERT: R 44 HIS cc_start: 0.4169 (m-70) cc_final: 0.3907 (t-90) REVERT: R 72 TRP cc_start: 0.6543 (m100) cc_final: 0.5838 (m100) REVERT: R 228 TYR cc_start: 0.7402 (m-80) cc_final: 0.7033 (m-80) REVERT: R 284 TYR cc_start: 0.1037 (m-10) cc_final: 0.0670 (m-80) outliers start: 52 outliers final: 29 residues processed: 330 average time/residue: 0.1512 time to fit residues: 76.7484 Evaluate side-chains 297 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 110 CYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3863 ILE 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 125 VAL Chi-restraints excluded: chain N residue 128 MET Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain R residue 51 VAL 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 4 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 192 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 181 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** 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 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.139491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.104361 restraints weight = 54209.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.104762 restraints weight = 32287.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.105318 restraints weight = 24296.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105450 restraints weight = 20717.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.105538 restraints weight = 19420.861| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21720 Z= 0.159 Angle : 0.662 9.540 30585 Z= 0.371 Chirality : 0.047 0.360 3438 Planarity : 0.004 0.076 2870 Dihedral : 27.780 178.363 5203 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.92 % Favored : 92.02 % Rotamer: Outliers : 3.64 % Allowed : 15.99 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.19), residues: 1830 helix: 1.60 (0.21), residues: 574 sheet: -2.07 (0.29), residues: 292 loop : -2.75 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 30 TYR 0.023 0.002 TYR H 37 PHE 0.017 0.001 PHE H 67 TRP 0.021 0.002 TRP R 156 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (21716) covalent geometry : angle 0.66212 / 0.37 (30585) hydrogen bonds : bond 0.05346 / 3.49 ( 898) hydrogen bonds : angle 3.87253 / 2.75 ( 2250) metal coordination : bond 0.00096 / 0.06 ( 2) Misc. bond : bond 0.00155 / 0.10 ( 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 337 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 279 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8839 (m) cc_final: 0.8519 (p) REVERT: E 73 GLU cc_start: 0.7825 (tt0) cc_final: 0.7596 (mt-10) REVERT: F 84 MET cc_start: 0.7261 (tpp) cc_final: 0.7059 (tpp) REVERT: F 88 TYR cc_start: 0.8668 (m-10) cc_final: 0.7439 (m-10) REVERT: H 80 TYR cc_start: 0.7339 (m-10) cc_final: 0.6432 (m-10) REVERT: H 82 LYS cc_start: 0.8477 (mttt) cc_final: 0.8185 (mttm) REVERT: K 3828 LYS cc_start: 0.7804 (pttt) cc_final: 0.7418 (pttm) REVERT: K 3876 ASP cc_start: 0.8207 (m-30) cc_final: 0.7824 (p0) REVERT: K 3938 GLU cc_start: 0.7384 (tt0) cc_final: 0.7071 (tm-30) REVERT: N 320 ILE cc_start: 0.9194 (mp) cc_final: 0.8803 (pt) REVERT: T 315 MET cc_start: 0.5362 (mtm) cc_final: 0.5131 (mtp) REVERT: T 500 MET cc_start: 0.0040 (ptm) cc_final: -0.0760 (ptm) REVERT: T 503 MET cc_start: 0.6402 (mmm) cc_final: 0.5509 (mpp) REVERT: R 72 TRP cc_start: 0.6623 (m100) cc_final: 0.5773 (m100) REVERT: R 228 TYR cc_start: 0.7477 (m-80) cc_final: 0.7112 (m-80) REVERT: R 284 TYR cc_start: 0.1066 (m-10) cc_final: 0.0658 (m-80) outliers start: 58 outliers final: 45 residues processed: 314 average time/residue: 0.1488 time to fit residues: 72.1129 Evaluate side-chains 308 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL 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 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 79 ILE 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 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 73 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 64 GLU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 THR 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 3848 ASN Chi-restraints excluded: chain K residue 3863 ILE Chi-restraints excluded: chain K residue 3867 GLN Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 81 LEU 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 222 ILE Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.0060 chunk 82 optimal weight: 30.0000 chunk 167 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 141 optimal weight: 0.0000 chunk 22 optimal weight: 6.9990 chunk 38 optimal weight: 0.0970 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN N 250 ASN N 273 GLN ** 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** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.141924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106431 restraints weight = 53607.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106880 restraints weight = 36019.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107216 restraints weight = 23231.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.107525 restraints weight = 21801.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108491 restraints weight = 19300.747| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 21720 Z= 0.132 Angle : 0.639 9.985 30585 Z= 0.360 Chirality : 0.046 0.369 3438 Planarity : 0.004 0.080 2870 Dihedral : 27.662 178.190 5203 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.63 % Allowed : 17.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.19), residues: 1830 helix: 1.84 (0.22), residues: 576 sheet: -1.98 (0.29), residues: 295 loop : -2.66 (0.18), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 30 TYR 0.026 0.001 TYR N 115 PHE 0.018 0.001 PHE N 189 TRP 0.021 0.002 TRP R 156 HIS 0.006 0.001 HIS K3898 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (21716) covalent geometry : angle 0.63857 / 0.36 (30585) hydrogen bonds : bond 0.04617 / 3.02 ( 898) hydrogen bonds : angle 3.58623 / 2.53 ( 2250) metal coordination : bond 0.00087 / 0.06 ( 2) Misc. bond : bond 0.00148 / 0.10 ( 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 335 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 293 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 118 THR cc_start: 0.8762 (m) cc_final: 0.8386 (p) REVERT: B 84 MET cc_start: 0.7411 (mmt) cc_final: 0.7115 (mmt) REVERT: E 73 GLU cc_start: 0.7793 (tt0) cc_final: 0.7579 (mt-10) REVERT: F 88 TYR cc_start: 0.8544 (m-10) cc_final: 0.7254 (m-10) REVERT: H 30 ARG cc_start: 0.8343 (mpt180) cc_final: 0.7528 (mmp80) REVERT: H 80 TYR cc_start: 0.7228 (m-10) cc_final: 0.7025 (m-80) REVERT: H 82 LYS cc_start: 0.8329 (mttt) cc_final: 0.7919 (mmtt) REVERT: K 3876 ASP cc_start: 0.8269 (m-30) cc_final: 0.7823 (p0) REVERT: K 3923 GLN cc_start: 0.8385 (pm20) cc_final: 0.8181 (pm20) REVERT: K 3938 GLU cc_start: 0.7255 (tt0) cc_final: 0.7040 (tm-30) REVERT: N 226 ASP cc_start: 0.8516 (t0) cc_final: 0.7730 (t0) REVERT: N 256 LYS cc_start: 0.8705 (tppt) cc_final: 0.8424 (tppt) REVERT: N 320 ILE cc_start: 0.9187 (mp) cc_final: 0.8835 (pt) REVERT: N 340 ASP cc_start: 0.8789 (t0) cc_final: 0.7960 (t0) REVERT: T 500 MET cc_start: -0.0167 (ptm) cc_final: -0.1028 (ptm) REVERT: T 503 MET cc_start: 0.6389 (mmm) cc_final: 0.5476 (mpp) REVERT: R 44 HIS cc_start: 0.4667 (m-70) cc_final: 0.4172 (t-90) REVERT: R 72 TRP cc_start: 0.6640 (m100) cc_final: 0.5741 (m100) REVERT: R 158 VAL cc_start: 0.7670 (m) cc_final: 0.7376 (p) REVERT: R 228 TYR cc_start: 0.7569 (m-80) cc_final: 0.7191 (m-80) REVERT: R 284 TYR cc_start: 0.1011 (m-10) cc_final: 0.0586 (m-80) outliers start: 42 outliers final: 35 residues processed: 320 average time/residue: 0.1445 time to fit residues: 72.2821 Evaluate side-chains 303 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 268 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 89 VAL 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 79 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 81 ASN 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 3867 GLN 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 53 PHE Chi-restraints excluded: chain N residue 81 LEU 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 257 CYS Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 222 PHE 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 188 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 41 optimal weight: 0.0670 chunk 91 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN 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 44 HIS ** 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 = 0.4188 r_free = 0.4188 target = 0.139886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.104962 restraints weight = 53766.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.105277 restraints weight = 31676.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.105821 restraints weight = 23583.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.105949 restraints weight = 19976.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.106066 restraints weight = 18661.027| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21720 Z= 0.156 Angle : 0.653 9.630 30585 Z= 0.363 Chirality : 0.046 0.353 3438 Planarity : 0.004 0.078 2870 Dihedral : 27.674 177.389 5203 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.32 % Allowed : 17.30 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.19), residues: 1830 helix: 1.62 (0.21), residues: 581 sheet: -1.89 (0.30), residues: 294 loop : -2.67 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.023 0.002 TYR H 37 PHE 0.013 0.001 PHE H 67 TRP 0.024 0.002 TRP R 156 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (21716) covalent geometry : angle 0.65339 / 0.36 (30585) hydrogen bonds : bond 0.05090 / 3.34 ( 898) hydrogen bonds : angle 3.73720 / 2.66 ( 2250) metal coordination : bond 0.00073 / 0.05 ( 2) Misc. bond : bond 0.00158 / 0.11 ( 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 310 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 257 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8841 (m) cc_final: 0.8585 (p) REVERT: C 84 GLN cc_start: 0.9674 (OUTLIER) cc_final: 0.9301 (tp40) REVERT: E 73 GLU cc_start: 0.7782 (tt0) cc_final: 0.7522 (mt-10) REVERT: F 84 MET cc_start: 0.7213 (tpp) cc_final: 0.6910 (tpp) REVERT: F 88 TYR cc_start: 0.8555 (m-10) cc_final: 0.7421 (m-10) REVERT: G 18 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.7891 (p) REVERT: H 30 ARG cc_start: 0.8368 (mpt180) cc_final: 0.7497 (mmp80) REVERT: H 56 MET cc_start: 0.8566 (tpp) cc_final: 0.8359 (tpp) REVERT: H 80 TYR cc_start: 0.7297 (m-10) cc_final: 0.6530 (m-10) REVERT: H 82 LYS cc_start: 0.8338 (mttt) cc_final: 0.7927 (mmtt) REVERT: K 3876 ASP cc_start: 0.8314 (m-30) cc_final: 0.7774 (p0) REVERT: K 3938 GLU cc_start: 0.7530 (tt0) cc_final: 0.7273 (tm-30) REVERT: N 226 ASP cc_start: 0.8650 (t0) cc_final: 0.7896 (t0) REVERT: N 256 LYS cc_start: 0.8679 (tppt) cc_final: 0.8420 (tppt) REVERT: N 320 ILE cc_start: 0.9173 (mp) cc_final: 0.8836 (pt) REVERT: N 340 ASP cc_start: 0.8843 (t0) cc_final: 0.8097 (t0) REVERT: T 500 MET cc_start: -0.0259 (ptm) cc_final: -0.1002 (ptm) REVERT: T 503 MET cc_start: 0.6362 (mmm) cc_final: 0.5471 (mpp) REVERT: R 72 TRP cc_start: 0.6570 (m100) cc_final: 0.5634 (m100) REVERT: R 228 TYR cc_start: 0.7555 (m-80) cc_final: 0.7294 (m-80) REVERT: R 284 TYR cc_start: 0.1151 (m-10) cc_final: 0.0772 (m-80) outliers start: 53 outliers final: 43 residues processed: 292 average time/residue: 0.1487 time to fit residues: 67.8395 Evaluate side-chains 298 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 89 VAL Chi-restraints excluded: chain A residue 110 CYS 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 23 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 73 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 64 GLU Chi-restraints excluded: chain G residue 85 LEU 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 3816 MET Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3867 GLN Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain K residue 3940 LEU Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 81 LEU 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 257 CYS Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 222 PHE 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 41 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 100 optimal weight: 30.0000 chunk 201 optimal weight: 40.0000 chunk 207 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN 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 44 HIS ** 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 = 0.4208 r_free = 0.4208 target = 0.141439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.107047 restraints weight = 54007.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.107198 restraints weight = 32099.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.107802 restraints weight = 24390.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.107968 restraints weight = 20583.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.108083 restraints weight = 19315.884| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21720 Z= 0.131 Angle : 0.640 11.649 30585 Z= 0.357 Chirality : 0.045 0.358 3438 Planarity : 0.004 0.080 2870 Dihedral : 27.614 177.556 5203 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.51 % Allowed : 18.68 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.20), residues: 1830 helix: 1.81 (0.22), residues: 581 sheet: -1.83 (0.30), residues: 300 loop : -2.65 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E 63 TYR 0.028 0.001 TYR H 37 PHE 0.013 0.001 PHE N 189 TRP 0.022 0.002 TRP R 156 HIS 0.009 0.001 HIS K3898 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (21716) covalent geometry : angle 0.64010 / 0.36 (30585) hydrogen bonds : bond 0.04660 / 3.03 ( 898) hydrogen bonds : angle 3.54026 / 2.52 ( 2250) metal coordination : bond 0.00113 / 0.08 ( 2) Misc. bond : bond 0.00152 / 0.10 ( 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 304 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 118 THR cc_start: 0.8804 (m) cc_final: 0.8588 (p) REVERT: C 84 GLN cc_start: 0.9640 (OUTLIER) cc_final: 0.9263 (tp40) REVERT: D 30 ARG cc_start: 0.7412 (mmm160) cc_final: 0.7012 (mtp85) REVERT: F 84 MET cc_start: 0.7279 (tpp) cc_final: 0.6969 (tpp) REVERT: F 88 TYR cc_start: 0.8544 (m-10) cc_final: 0.7285 (m-10) REVERT: G 18 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.7900 (p) REVERT: H 30 ARG cc_start: 0.8343 (mpt180) cc_final: 0.7460 (mmp80) REVERT: H 80 TYR cc_start: 0.7240 (m-10) cc_final: 0.7008 (m-80) REVERT: H 82 LYS cc_start: 0.8318 (mttt) cc_final: 0.7909 (mmtt) REVERT: K 3876 ASP cc_start: 0.8356 (m-30) cc_final: 0.7742 (p0) REVERT: K 3931 MET cc_start: 0.7019 (tpp) cc_final: 0.6602 (tpp) REVERT: K 3938 GLU cc_start: 0.7439 (tt0) cc_final: 0.7132 (tm-30) REVERT: N 226 ASP cc_start: 0.8584 (t0) cc_final: 0.7848 (t0) REVERT: N 256 LYS cc_start: 0.8669 (tppt) cc_final: 0.8404 (tppt) REVERT: N 320 ILE cc_start: 0.9166 (mp) cc_final: 0.8847 (pt) REVERT: N 340 ASP cc_start: 0.8864 (t0) cc_final: 0.8041 (t0) REVERT: T 336 MET cc_start: 0.3763 (mmm) cc_final: 0.2920 (mmm) REVERT: T 500 MET cc_start: -0.0252 (ptm) cc_final: -0.0981 (ptm) REVERT: T 503 MET cc_start: 0.6364 (mmm) cc_final: 0.5473 (mpp) REVERT: R 72 TRP cc_start: 0.6603 (m100) cc_final: 0.5657 (m100) REVERT: R 158 VAL cc_start: 0.7694 (m) cc_final: 0.7389 (p) REVERT: R 228 TYR cc_start: 0.7589 (m-80) cc_final: 0.7366 (m-80) REVERT: R 284 TYR cc_start: 0.1323 (m-10) cc_final: 0.0911 (m-80) outliers start: 40 outliers final: 34 residues processed: 292 average time/residue: 0.1478 time to fit residues: 67.3915 Evaluate side-chains 295 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 89 VAL Chi-restraints excluded: chain A residue 110 CYS 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 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain E residue 80 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 85 LEU Chi-restraints excluded: chain H residue 81 ASN 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 3867 GLN 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 49 VAL Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 144 ILE 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 15 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 152 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 76 optimal weight: 30.0000 chunk 12 optimal weight: 0.9980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN 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 44 HIS ** 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 = 0.4191 r_free = 0.4191 target = 0.140138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102169 restraints weight = 53863.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102787 restraints weight = 37923.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.103348 restraints weight = 24252.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103806 restraints weight = 20854.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.104280 restraints weight = 19859.655| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21720 Z= 0.153 Angle : 0.655 10.062 30585 Z= 0.361 Chirality : 0.046 0.346 3438 Planarity : 0.004 0.077 2870 Dihedral : 27.616 176.866 5203 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.13 % Allowed : 19.25 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.19), residues: 1830 helix: 1.68 (0.21), residues: 580 sheet: -1.79 (0.30), residues: 300 loop : -2.65 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.024 0.002 TYR D 37 PHE 0.013 0.001 PHE K3885 TRP 0.022 0.002 TRP R 156 HIS 0.006 0.001 HIS K3898 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (21716) covalent geometry : angle 0.65457 / 0.36 (30585) hydrogen bonds : bond 0.05013 / 3.28 ( 898) hydrogen bonds : angle 3.65443 / 2.61 ( 2250) metal coordination : bond 0.00091 / 0.06 ( 2) Misc. bond : bond 0.00153 / 0.10 ( 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 292 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 GLN cc_start: 0.9671 (OUTLIER) cc_final: 0.9284 (tp40) REVERT: D 48 ASP cc_start: 0.6574 (t0) cc_final: 0.6237 (t0) REVERT: F 84 MET cc_start: 0.7362 (tpp) cc_final: 0.7010 (tpp) REVERT: F 88 TYR cc_start: 0.8595 (m-10) cc_final: 0.7683 (m-10) REVERT: G 18 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.7948 (p) REVERT: H 30 ARG cc_start: 0.8290 (mpt180) cc_final: 0.7419 (mmp80) REVERT: H 80 TYR cc_start: 0.7238 (m-10) cc_final: 0.6605 (m-10) REVERT: H 82 LYS cc_start: 0.8319 (mttt) cc_final: 0.8061 (mttm) REVERT: K 3876 ASP cc_start: 0.8431 (m-30) cc_final: 0.7808 (p0) REVERT: K 3938 GLU cc_start: 0.7251 (tt0) cc_final: 0.6937 (tm-30) REVERT: N 226 ASP cc_start: 0.8555 (t0) cc_final: 0.7836 (t0) REVERT: N 256 LYS cc_start: 0.8693 (tppt) cc_final: 0.8431 (tppt) REVERT: N 320 ILE cc_start: 0.9238 (mp) cc_final: 0.8909 (pt) REVERT: N 340 ASP cc_start: 0.8899 (t0) cc_final: 0.8082 (t0) REVERT: T 500 MET cc_start: -0.0451 (ptm) cc_final: -0.1355 (ptm) REVERT: T 503 MET cc_start: 0.6366 (mmm) cc_final: 0.5364 (mpp) REVERT: R 72 TRP cc_start: 0.6912 (m100) cc_final: 0.5827 (m100) REVERT: R 140 GLN cc_start: 0.4680 (mm-40) cc_final: 0.4468 (mm-40) REVERT: R 228 TYR cc_start: 0.7852 (m-80) cc_final: 0.7542 (m-80) REVERT: R 284 TYR cc_start: 0.1442 (m-10) cc_final: 0.1154 (m-80) outliers start: 34 outliers final: 29 residues processed: 282 average time/residue: 0.1521 time to fit residues: 66.6303 Evaluate side-chains 286 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 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 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 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 85 LEU Chi-restraints excluded: chain H residue 81 ASN 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 3867 GLN Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain T residue 476 LYS Chi-restraints excluded: chain R residue 51 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 15 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 191 optimal weight: 0.0670 chunk 201 optimal weight: 40.0000 chunk 159 optimal weight: 0.1980 chunk 73 optimal weight: 40.0000 chunk 200 optimal weight: 4.9990 chunk 202 optimal weight: 8.9990 overall best weight: 2.6524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN F 25 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN N 250 ASN N 273 GLN ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.139435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102440 restraints weight = 53683.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102719 restraints weight = 38957.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102776 restraints weight = 25949.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.103200 restraints weight = 22716.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.103431 restraints weight = 20452.881| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21720 Z= 0.167 Angle : 0.673 10.741 30585 Z= 0.371 Chirality : 0.046 0.347 3438 Planarity : 0.004 0.079 2870 Dihedral : 27.600 176.923 5203 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.38 % Allowed : 19.44 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.19), residues: 1830 helix: 1.53 (0.21), residues: 581 sheet: -1.79 (0.30), residues: 302 loop : -2.64 (0.18), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 92 TYR 0.031 0.002 TYR H 37 PHE 0.015 0.001 PHE K3885 TRP 0.020 0.002 TRP R 156 HIS 0.011 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (21716) covalent geometry : angle 0.67311 / 0.37 (30585) hydrogen bonds : bond 0.05321 / 3.48 ( 898) hydrogen bonds : angle 3.72321 / 2.67 ( 2250) metal coordination : bond 0.00144 / 0.10 ( 2) Misc. bond : bond 0.00181 / 0.12 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3402.02 seconds wall clock time: 59 minutes 43.07 seconds (3583.07 seconds total)