Starting phenix.real_space_refine on Fri Aug 9 22:32:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/08_2024/6kiv_9999.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/08_2024/6kiv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/08_2024/6kiv_9999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/08_2024/6kiv_9999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/08_2024/6kiv_9999.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/08_2024/6kiv_9999.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8596 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 290 5.49 5 S 61 5.16 5 C 12166 2.51 5 N 3759 2.21 5 O 4442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 3916": "NH1" <-> "NH2" Residue "K ARG 3936": "NH1" <-> "NH2" Residue "K ARG 3965": "NH1" <-> "NH2" Residue "N ARG 76": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N ARG 190": "NH1" <-> "NH2" Residue "N ARG 228": "NH1" <-> "NH2" Residue "N ARG 272": "NH1" <-> "NH2" Residue "T TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20719 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "D" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1434 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2881 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 14, 'TRANS': 351} Chain breaks: 1 Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "T" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1399 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 12, 'TRANS': 163} Chain breaks: 1 Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2326 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: 11.55, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 9.47 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3957 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 35 sheets defined 31.8% alpha, 13.0% beta 145 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 8.77 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.554A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.997A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.858A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.671A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.917A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.843A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 4.083A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.201A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.554A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.997A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.672A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 4.145A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.461A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.771A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.664A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 4.034A pdb=" N ALA H 121 " --> pdb=" O CYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 3815 through 3830 removed outlier: 3.755A pdb=" N ARG K3819 " --> pdb=" O PRO K3815 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS K3828 " --> pdb=" O LYS K3824 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU K3829 " --> pdb=" O LYS K3825 " (cutoff:3.500A) Processing helix chain 'K' and resid 3866 through 3878 removed outlier: 4.719A pdb=" N LYS K3870 " --> pdb=" O ILE K3866 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'O' and resid 22 through 34 removed outlier: 3.827A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 41 removed outlier: 4.187A pdb=" N GLN O 41 " --> pdb=" O PRO O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 59 removed outlier: 3.536A pdb=" N ASP O 58 " --> pdb=" O THR O 55 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR O 59 " --> pdb=" O LEU O 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 59' Processing helix chain 'T' and resid 501 through 503 No H-bonds generated for 'chain 'T' and resid 501 through 503' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.620A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.424A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.396A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.116A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.816A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'K' and resid 3831 through 3835 removed outlier: 4.089A pdb=" N GLY K3832 " --> pdb=" O PHE K3844 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 3884 through 3886 Processing sheet with id=AA8, first strand: chain 'K' and resid 3898 through 3899 removed outlier: 3.608A pdb=" N GLY K3899 " --> pdb=" O LYS N 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 3906 through 3907 removed outlier: 6.746A pdb=" N ASN K3906 " --> pdb=" O TYR K3942 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 3915 through 3920 removed outlier: 3.951A pdb=" N ARG K3916 " --> pdb=" O VAL K3927 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL K3927 " --> pdb=" O ARG K3916 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE K3918 " --> pdb=" O HIS K3925 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS K3925 " --> pdb=" O ILE K3918 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE K3920 " --> pdb=" O GLN K3923 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN K3923 " --> pdb=" O ILE K3920 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'N' and resid 30 through 32 removed outlier: 3.586A pdb=" N THR N 31 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 69 through 73 removed outlier: 3.852A pdb=" N SER N 71 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA N 84 " --> pdb=" O SER N 71 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER N 83 " --> pdb=" O SER N 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 113 through 115 removed outlier: 3.790A pdb=" N GLN N 114 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL N 123 " --> pdb=" O LEU N 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.540A pdb=" N THR N 168 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 201 through 205 removed outlier: 7.131A pdb=" N ASN N 216 " --> pdb=" O LYS N 202 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE N 204 " --> pdb=" O LEU N 214 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU N 214 " --> pdb=" O ILE N 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 254 through 259 removed outlier: 6.977A pdb=" N GLY N 269 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N CYS N 257 " --> pdb=" O VAL N 267 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL N 267 " --> pdb=" O CYS N 257 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE N 259 " --> pdb=" O TYR N 265 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR N 265 " --> pdb=" O PHE N 259 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU N 276 " --> pdb=" O ILE N 289 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE N 289 " --> pdb=" O LEU N 276 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE N 278 " --> pdb=" O VAL N 287 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 310 through 311 removed outlier: 3.968A pdb=" N ILE N 310 " --> pdb=" O TRP N 321 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP N 321 " --> pdb=" O ILE N 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'O' and resid 12 through 16 removed outlier: 8.104A pdb=" N LEU O 67 " --> pdb=" O GLN O 2 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 43 through 45 removed outlier: 4.114A pdb=" N LEU O 43 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 306 through 308 removed outlier: 3.722A pdb=" N VAL T 480 " --> pdb=" O VAL T 307 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 314 through 316 removed outlier: 3.545A pdb=" N VAL T 316 " --> pdb=" O ILE T 472 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 396 through 398 removed outlier: 4.781A pdb=" N ILE T 396 " --> pdb=" O TRP T 327 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP T 327 " --> pdb=" O ILE T 396 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU T 398 " --> pdb=" O GLY T 325 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY T 325 " --> pdb=" O LEU T 398 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA T 326 " --> pdb=" O ARG T 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'T' and resid 331 through 332 Processing sheet with id=AC6, first strand: chain 'T' and resid 346 through 347 Processing sheet with id=AC7, first strand: chain 'T' and resid 372 through 374 removed outlier: 3.581A pdb=" N LYS T 380 " --> pdb=" O LYS T 373 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 448 through 450 removed outlier: 4.483A pdb=" N GLY T 457 " --> pdb=" O PHE T 449 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 36 through 37 Processing sheet with id=AD1, first strand: chain 'R' and resid 41 through 42 Processing sheet with id=AD2, first strand: chain 'R' and resid 48 through 53 removed outlier: 4.260A pdb=" N LYS R 52 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA R 61 " --> pdb=" O LYS R 52 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS R 70 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU R 68 " --> pdb=" O SER R 64 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 90 through 93 removed outlier: 3.783A pdb=" N ASP R 92 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS R 112 " --> pdb=" O SER R 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 136 through 137 removed outlier: 3.700A pdb=" N ASN R 136 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 177 through 179 removed outlier: 6.091A pdb=" N CYS R 195 " --> pdb=" O THR R 208 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR R 208 " --> pdb=" O CYS R 195 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE R 197 " --> pdb=" O LEU R 206 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 219 through 222 removed outlier: 3.615A pdb=" N LYS R 239 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 264 through 266 Processing sheet with id=AD8, first strand: chain 'R' and resid 304 through 309 removed outlier: 3.519A pdb=" N ALA R 308 " --> pdb=" O ALA R 317 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1506 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 9.40 Time building geometry restraints manager: 10.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4052 1.33 - 1.45: 6267 1.45 - 1.57: 10731 1.57 - 1.69: 578 1.69 - 1.81: 88 Bond restraints: 21716 Sorted by residual: bond pdb=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.375 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" C2 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.330 1.378 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C6 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.338 1.386 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.491 -0.069 3.00e-02 1.11e+03 5.28e+00 ... (remaining 21711 not shown) Histogram of bond angle deviations from ideal: 89.61 - 98.52: 10 98.52 - 107.43: 2740 107.43 - 116.34: 13589 116.34 - 125.25: 13075 125.25 - 134.15: 1171 Bond angle restraints: 30585 Sorted by residual: angle pdb=" CG SAH K4001 " pdb=" SD SAH K4001 " pdb=" C5' SAH K4001 " ideal model delta sigma weight residual 101.77 89.61 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 122.48 -9.30 2.37e+00 1.78e-01 1.54e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 125.89 -5.69 1.50e+00 4.44e-01 1.44e+01 angle pdb=" CA ARG G 99 " pdb=" CB ARG G 99 " pdb=" CG ARG G 99 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N GLN N 323 " pdb=" CA GLN N 323 " pdb=" C GLN N 323 " ideal model delta sigma weight residual 110.80 118.14 -7.34 2.13e+00 2.20e-01 1.19e+01 ... (remaining 30580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 10875 35.82 - 71.65: 1373 71.65 - 107.47: 25 107.47 - 143.29: 4 143.29 - 179.11: 1 Dihedral angle restraints: 12278 sinusoidal: 6877 harmonic: 5401 Sorted by residual: dihedral pdb=" CA LYS B 31 " pdb=" C LYS B 31 " pdb=" N PRO B 32 " pdb=" CA PRO B 32 " ideal model delta harmonic sigma weight residual 180.00 133.83 46.17 0 5.00e+00 4.00e-02 8.53e+01 dihedral pdb=" CA ASN K3779 " pdb=" C ASN K3779 " pdb=" N PHE K3780 " pdb=" CA PHE K3780 " ideal model delta harmonic sigma weight residual 180.00 138.88 41.12 0 5.00e+00 4.00e-02 6.76e+01 dihedral pdb=" CA TYR N 13 " pdb=" C TYR N 13 " pdb=" N PRO N 14 " pdb=" CA PRO N 14 " ideal model delta harmonic sigma weight residual -180.00 -143.60 -36.40 0 5.00e+00 4.00e-02 5.30e+01 ... (remaining 12275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2253 0.046 - 0.092: 872 0.092 - 0.138: 258 0.138 - 0.184: 49 0.184 - 0.230: 6 Chirality restraints: 3438 Sorted by residual: chirality pdb=" C1' SAH K4001 " pdb=" C2' SAH K4001 " pdb=" N9 SAH K4001 " pdb=" O4' SAH K4001 " both_signs ideal model delta sigma weight residual False 2.35 2.58 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3435 not shown) Planarity restraints: 2870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO B 32 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN K3779 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" CG ASN K3779 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN K3779 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN K3779 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K3768 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C VAL K3768 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL K3768 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS K3769 " -0.015 2.00e-02 2.50e+03 ... (remaining 2867 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4488 2.79 - 3.32: 17385 3.32 - 3.85: 37394 3.85 - 4.37: 41446 4.37 - 4.90: 64179 Nonbonded interactions: 164892 Sorted by model distance: nonbonded pdb=" OG SER R 129 " pdb=" OD2 ASP R 150 " model vdw 2.263 3.040 nonbonded pdb=" OG SER R 96 " pdb=" OD1 ASP R 98 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.265 3.040 nonbonded pdb=" OG SER R 49 " pdb=" O SER R 63 " model vdw 2.268 3.040 ... (remaining 164887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = (chain 'H' and resid 28 through 120) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.140 Set scattering table: 0.220 Process input model: 66.660 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 21716 Z= 0.424 Angle : 0.904 12.590 30585 Z= 0.511 Chirality : 0.053 0.230 3438 Planarity : 0.007 0.108 2870 Dihedral : 22.703 179.114 8794 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.16), residues: 1830 helix: -1.38 (0.17), residues: 568 sheet: -2.89 (0.26), residues: 312 loop : -3.18 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP N 303 HIS 0.010 0.002 HIS B 75 PHE 0.023 0.003 PHE N 189 TYR 0.031 0.003 TYR B 51 ARG 0.009 0.001 ARG F 39 *********************** 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 fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9254 (p) cc_final: 0.8948 (p) REVERT: A 123 ASP cc_start: 0.8318 (m-30) cc_final: 0.8094 (m-30) REVERT: B 35 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8090 (ttm-80) REVERT: B 58 LEU cc_start: 0.8871 (tp) cc_final: 0.8573 (tt) REVERT: B 92 ARG cc_start: 0.8717 (mtp-110) cc_final: 0.8398 (mtp-110) REVERT: D 27 ARG cc_start: 0.7875 (tmt170) cc_final: 0.7629 (tmt-80) REVERT: D 54 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8811 (mmmm) REVERT: D 65 ASP cc_start: 0.8143 (t0) cc_final: 0.7866 (t0) REVERT: D 81 ASN cc_start: 0.8438 (m-40) cc_final: 0.8148 (m110) REVERT: D 88 SER cc_start: 0.9070 (p) cc_final: 0.8866 (p) REVERT: F 88 TYR cc_start: 0.8891 (m-10) cc_final: 0.7805 (m-10) REVERT: G 18 SER cc_start: 0.8315 (m) cc_final: 0.7614 (p) REVERT: G 42 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7727 (mtm-85) REVERT: G 61 GLU cc_start: 0.8672 (tp30) cc_final: 0.8331 (tm-30) REVERT: H 73 GLU cc_start: 0.8267 (tp30) cc_final: 0.8037 (mt-10) REVERT: H 80 TYR cc_start: 0.7333 (m-10) cc_final: 0.6582 (m-10) REVERT: H 82 LYS cc_start: 0.8942 (mttt) cc_final: 0.8089 (mmtt) REVERT: K 3828 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8215 (pttt) REVERT: K 3846 LYS cc_start: 0.6392 (mtmt) cc_final: 0.6074 (tmtt) REVERT: N 60 LYS cc_start: 0.8170 (tptt) cc_final: 0.7547 (tppt) REVERT: N 115 TYR cc_start: 0.5656 (m-80) cc_final: 0.5121 (m-10) REVERT: N 226 ASP cc_start: 0.7903 (t0) cc_final: 0.7649 (t0) REVERT: N 320 ILE cc_start: 0.8932 (mp) cc_final: 0.8636 (pt) REVERT: T 503 MET cc_start: 0.6152 (mmm) cc_final: 0.5486 (mtm) REVERT: R 72 TRP cc_start: 0.6754 (m100) cc_final: 0.5447 (m100) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.4342 time to fit residues: 310.3957 Evaluate side-chains 290 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 20.0000 chunk 157 optimal weight: 0.0050 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 63 optimal weight: 0.0040 chunk 99 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 188 optimal weight: 20.0000 overall best weight: 1.7610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS C 38 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 81 ASN F 25 ASN G 89 ASN G 110 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 HIS N 273 GLN N 328 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 375 HIS T 381 HIS ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21716 Z= 0.212 Angle : 0.655 12.495 30585 Z= 0.369 Chirality : 0.041 0.159 3438 Planarity : 0.005 0.085 2870 Dihedral : 27.576 177.847 5203 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.26 % Allowed : 10.97 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.18), residues: 1830 helix: 0.60 (0.21), residues: 573 sheet: -2.54 (0.27), residues: 296 loop : -2.95 (0.17), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 156 HIS 0.013 0.001 HIS R 44 PHE 0.019 0.002 PHE N 189 TYR 0.027 0.002 TYR B 51 ARG 0.005 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 347 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8573 (m-30) cc_final: 0.8326 (m-30) REVERT: B 92 ARG cc_start: 0.8596 (mtp-110) cc_final: 0.8328 (ttp80) REVERT: D 44 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8310 (tm-30) REVERT: D 54 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8771 (mmmt) REVERT: D 81 ASN cc_start: 0.8525 (m110) cc_final: 0.8237 (m110) REVERT: D 88 SER cc_start: 0.8919 (p) cc_final: 0.8608 (p) REVERT: E 73 GLU cc_start: 0.8194 (tt0) cc_final: 0.7718 (tt0) REVERT: F 25 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7506 (t0) REVERT: F 64 ASN cc_start: 0.8951 (t0) cc_final: 0.8645 (t0) REVERT: F 88 TYR cc_start: 0.8789 (m-10) cc_final: 0.8475 (m-10) REVERT: F 92 ARG cc_start: 0.8682 (mtp-110) cc_final: 0.8397 (ttp80) REVERT: H 82 LYS cc_start: 0.8530 (mttt) cc_final: 0.7938 (mmtt) REVERT: K 3846 LYS cc_start: 0.6661 (mtmt) cc_final: 0.6065 (tmtt) REVERT: K 3873 LYS cc_start: 0.8059 (ptmt) cc_final: 0.7625 (ptpp) REVERT: K 3876 ASP cc_start: 0.8307 (m-30) cc_final: 0.7585 (p0) REVERT: N 51 TRP cc_start: 0.4878 (t60) cc_final: 0.3674 (t60) REVERT: N 128 MET cc_start: 0.7913 (ttm) cc_final: 0.7699 (ttm) REVERT: N 226 ASP cc_start: 0.8080 (t0) cc_final: 0.7534 (t0) REVERT: N 320 ILE cc_start: 0.8943 (mp) cc_final: 0.8610 (pt) REVERT: T 503 MET cc_start: 0.6358 (mmm) cc_final: 0.5864 (mpp) REVERT: R 72 TRP cc_start: 0.6464 (m100) cc_final: 0.5037 (m100) outliers start: 52 outliers final: 32 residues processed: 383 average time/residue: 0.3569 time to fit residues: 202.0978 Evaluate side-chains 300 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 267 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 220 ARG Chi-restraints excluded: chain N residue 233 CYS Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 157 optimal weight: 0.1980 chunk 128 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 84 GLN D 79 HIS ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 250 ASN N 273 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21716 Z= 0.238 Angle : 0.645 9.808 30585 Z= 0.360 Chirality : 0.041 0.196 3438 Planarity : 0.004 0.081 2870 Dihedral : 27.453 178.086 5203 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.39 % Allowed : 12.98 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.19), residues: 1830 helix: 1.30 (0.21), residues: 578 sheet: -2.31 (0.28), residues: 294 loop : -2.85 (0.17), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 59 HIS 0.009 0.001 HIS R 44 PHE 0.019 0.002 PHE N 189 TYR 0.020 0.002 TYR N 13 ARG 0.004 0.000 ARG N 190 *********************** 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 369 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 299 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8536 (m-30) cc_final: 0.8282 (m-30) REVERT: B 44 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8360 (mtmt) REVERT: B 92 ARG cc_start: 0.8719 (mtp-110) cc_final: 0.8269 (ttp80) REVERT: D 44 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8382 (tm-30) REVERT: D 48 ASP cc_start: 0.6840 (t0) cc_final: 0.6528 (t0) REVERT: D 54 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8823 (mmmt) REVERT: D 81 ASN cc_start: 0.8545 (m110) cc_final: 0.8240 (m110) REVERT: E 73 GLU cc_start: 0.7894 (tt0) cc_final: 0.7689 (tt0) REVERT: F 25 ASN cc_start: 0.8183 (t0) cc_final: 0.7953 (t0) REVERT: F 64 ASN cc_start: 0.9000 (t0) cc_final: 0.8703 (t0) REVERT: F 84 MET cc_start: 0.7361 (tpp) cc_final: 0.6981 (tpp) REVERT: F 88 TYR cc_start: 0.8668 (m-10) cc_final: 0.7319 (m-10) REVERT: F 92 ARG cc_start: 0.8765 (mtp-110) cc_final: 0.8417 (ttp80) REVERT: G 18 SER cc_start: 0.8508 (m) cc_final: 0.7968 (p) REVERT: H 40 LYS cc_start: 0.9098 (mptt) cc_final: 0.8888 (mptt) REVERT: H 80 TYR cc_start: 0.7215 (m-10) cc_final: 0.6541 (m-80) REVERT: H 82 LYS cc_start: 0.8505 (mttt) cc_final: 0.7937 (mmtt) REVERT: K 3846 LYS cc_start: 0.6597 (mtmt) cc_final: 0.5966 (tptp) REVERT: K 3898 HIS cc_start: 0.7699 (m-70) cc_final: 0.6804 (m-70) REVERT: N 51 TRP cc_start: 0.4792 (t60) cc_final: 0.3673 (t60) REVERT: N 320 ILE cc_start: 0.8954 (mp) cc_final: 0.8644 (pt) REVERT: N 339 LEU cc_start: 0.8543 (pp) cc_final: 0.8323 (pp) REVERT: T 346 TRP cc_start: 0.2499 (OUTLIER) cc_final: 0.1969 (m100) REVERT: T 468 TYR cc_start: 0.3245 (m-80) cc_final: 0.2745 (m-80) REVERT: T 500 MET cc_start: 0.0186 (ptm) cc_final: -0.0475 (ptm) REVERT: T 503 MET cc_start: 0.6321 (mmm) cc_final: 0.5471 (mpp) REVERT: R 72 TRP cc_start: 0.6473 (m100) cc_final: 0.5698 (m100) REVERT: R 284 TYR cc_start: 0.1160 (m-10) cc_final: 0.0769 (m-80) outliers start: 70 outliers final: 44 residues processed: 344 average time/residue: 0.3417 time to fit residues: 177.1522 Evaluate side-chains 315 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 270 time to evaluate : 1.837 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3863 ILE Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 233 CYS Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 346 TRP Chi-restraints excluded: chain T residue 384 SER Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP 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 186 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 201 optimal weight: 50.0000 chunk 99 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 HIS E 55 GLN E 113 HIS F 75 HIS ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 21716 Z= 0.483 Angle : 0.820 11.831 30585 Z= 0.448 Chirality : 0.048 0.263 3438 Planarity : 0.006 0.080 2870 Dihedral : 27.884 178.532 5203 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 5.52 % Allowed : 13.67 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.18), residues: 1830 helix: 0.58 (0.21), residues: 570 sheet: -2.49 (0.29), residues: 263 loop : -2.91 (0.17), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP N 279 HIS 0.024 0.002 HIS K3898 PHE 0.028 0.003 PHE K3885 TYR 0.032 0.003 TYR N 13 ARG 0.007 0.001 ARG E 116 *********************** 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 361 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 273 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8699 (m) cc_final: 0.8403 (p) REVERT: A 123 ASP cc_start: 0.8550 (m-30) cc_final: 0.8294 (m-30) REVERT: A 125 GLN cc_start: 0.7733 (mt0) cc_final: 0.7395 (mm110) REVERT: C 56 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: C 73 ASN cc_start: 0.8716 (t0) cc_final: 0.8516 (t0) REVERT: D 48 ASP cc_start: 0.7086 (t0) cc_final: 0.6672 (t0) REVERT: D 54 LYS cc_start: 0.9279 (mmmt) cc_final: 0.9041 (mmmt) REVERT: D 81 ASN cc_start: 0.8761 (m110) cc_final: 0.8496 (m110) REVERT: F 31 LYS cc_start: 0.9325 (tppt) cc_final: 0.9017 (tppt) REVERT: F 88 TYR cc_start: 0.8730 (m-10) cc_final: 0.8445 (m-10) REVERT: F 92 ARG cc_start: 0.8960 (mtp-110) cc_final: 0.8664 (ttp80) REVERT: G 84 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: H 30 ARG cc_start: 0.8374 (mpt180) cc_final: 0.7617 (mmp80) REVERT: H 82 LYS cc_start: 0.8534 (mttt) cc_final: 0.8235 (mttm) REVERT: K 3781 LEU cc_start: 0.6956 (mt) cc_final: 0.6748 (mt) REVERT: K 3845 CYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8626 (m) REVERT: K 3876 ASP cc_start: 0.8622 (m-30) cc_final: 0.8048 (p0) REVERT: K 3940 LEU cc_start: 0.8721 (mm) cc_final: 0.8172 (mm) REVERT: N 226 ASP cc_start: 0.8402 (t0) cc_final: 0.7632 (t0) REVERT: N 320 ILE cc_start: 0.9147 (mp) cc_final: 0.8893 (pt) REVERT: T 468 TYR cc_start: 0.3236 (m-80) cc_final: 0.2681 (m-80) REVERT: T 500 MET cc_start: -0.0082 (ptm) cc_final: -0.1131 (ptm) REVERT: T 503 MET cc_start: 0.6175 (mmm) cc_final: 0.5629 (mpp) REVERT: R 72 TRP cc_start: 0.6338 (m100) cc_final: 0.5630 (m100) REVERT: R 228 TYR cc_start: 0.7399 (m-80) cc_final: 0.7046 (m-80) outliers start: 88 outliers final: 63 residues processed: 331 average time/residue: 0.3090 time to fit residues: 158.2984 Evaluate side-chains 312 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 246 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 21 VAL 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 85 ASP 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 56 GLU 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 51 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 82 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 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3839 HIS 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 3866 ILE Chi-restraints excluded: chain K residue 3867 GLN Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL 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 252 THR Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 309 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 0.4980 chunk 114 optimal weight: 0.0470 chunk 2 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 171 optimal weight: 30.0000 chunk 138 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 180 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** K3867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 250 ASN N 273 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 354 GLN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS R 255 HIS R 295 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21716 Z= 0.170 Angle : 0.614 10.122 30585 Z= 0.344 Chirality : 0.040 0.197 3438 Planarity : 0.004 0.069 2870 Dihedral : 27.409 174.595 5203 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.01 % Allowed : 17.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.19), residues: 1830 helix: 1.64 (0.21), residues: 580 sheet: -2.27 (0.28), residues: 293 loop : -2.72 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 156 HIS 0.008 0.001 HIS R 44 PHE 0.018 0.001 PHE N 189 TYR 0.039 0.002 TYR K3875 ARG 0.006 0.000 ARG K3903 *********************** 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 350 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 302 time to evaluate : 1.806 Fit side-chains REVERT: A 105 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8322 (tm-30) REVERT: A 118 THR cc_start: 0.8600 (m) cc_final: 0.8393 (p) REVERT: A 123 ASP cc_start: 0.8535 (m-30) cc_final: 0.8330 (m-30) REVERT: D 30 ARG cc_start: 0.7336 (mtp85) cc_final: 0.7118 (mtp85) REVERT: D 48 ASP cc_start: 0.6975 (t0) cc_final: 0.6574 (t0) REVERT: D 54 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8818 (mmmm) REVERT: D 81 ASN cc_start: 0.8390 (m110) cc_final: 0.8124 (m110) REVERT: F 25 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.7963 (t0) REVERT: F 84 MET cc_start: 0.7192 (tpp) cc_final: 0.6956 (tpp) REVERT: F 92 ARG cc_start: 0.8730 (mtp-110) cc_final: 0.8480 (ttp80) REVERT: G 92 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6942 (mm-30) REVERT: H 30 ARG cc_start: 0.8379 (mpt180) cc_final: 0.7643 (mmp80) REVERT: H 80 TYR cc_start: 0.7155 (m-10) cc_final: 0.6896 (m-80) REVERT: H 82 LYS cc_start: 0.8339 (mttt) cc_final: 0.7861 (mmtt) REVERT: K 3876 ASP cc_start: 0.8602 (m-30) cc_final: 0.7813 (p0) REVERT: N 226 ASP cc_start: 0.8200 (t0) cc_final: 0.7369 (t0) REVERT: N 320 ILE cc_start: 0.8937 (mp) cc_final: 0.8667 (pt) REVERT: N 339 LEU cc_start: 0.8502 (pp) cc_final: 0.8246 (pp) REVERT: T 500 MET cc_start: -0.0130 (ptm) cc_final: -0.1048 (ptm) REVERT: T 503 MET cc_start: 0.6145 (mmm) cc_final: 0.5603 (mpp) REVERT: R 72 TRP cc_start: 0.6172 (m100) cc_final: 0.5236 (m100) REVERT: R 140 GLN cc_start: 0.5169 (mt0) cc_final: 0.4508 (mm110) REVERT: R 228 TYR cc_start: 0.7270 (m-80) cc_final: 0.7002 (m-80) REVERT: R 230 LEU cc_start: 0.6270 (tp) cc_final: 0.5630 (tp) outliers start: 48 outliers final: 32 residues processed: 330 average time/residue: 0.3281 time to fit residues: 165.4515 Evaluate side-chains 296 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 263 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain K residue 3946 PHE Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 222 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 201 optimal weight: 40.0000 chunk 167 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3925 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS R 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21716 Z= 0.200 Angle : 0.617 10.370 30585 Z= 0.343 Chirality : 0.040 0.205 3438 Planarity : 0.004 0.076 2870 Dihedral : 27.415 176.702 5203 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.64 % Allowed : 17.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.19), residues: 1830 helix: 1.81 (0.22), residues: 575 sheet: -2.06 (0.28), residues: 318 loop : -2.64 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 156 HIS 0.006 0.001 HIS K3898 PHE 0.012 0.001 PHE N 189 TYR 0.023 0.002 TYR D 80 ARG 0.010 0.000 ARG R 181 *********************** 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 327 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 269 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8314 (tm-30) REVERT: A 120 MET cc_start: 0.7360 (mmt) cc_final: 0.7150 (mmm) REVERT: A 123 ASP cc_start: 0.8542 (m-30) cc_final: 0.8288 (m-30) REVERT: B 84 MET cc_start: 0.7876 (mmt) cc_final: 0.7586 (tpt) REVERT: C 56 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7218 (tp30) REVERT: D 48 ASP cc_start: 0.6941 (t0) cc_final: 0.6522 (t0) REVERT: D 54 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8901 (mmmt) REVERT: D 81 ASN cc_start: 0.8406 (m110) cc_final: 0.8142 (m110) REVERT: F 25 ASN cc_start: 0.8475 (t0) cc_final: 0.8107 (t0) REVERT: F 88 TYR cc_start: 0.8592 (m-10) cc_final: 0.7674 (m-10) REVERT: F 92 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8572 (ttp80) REVERT: G 18 SER cc_start: 0.8654 (OUTLIER) cc_final: 0.7990 (p) REVERT: H 30 ARG cc_start: 0.8354 (mpt180) cc_final: 0.7723 (mmp80) REVERT: H 40 LYS cc_start: 0.9080 (mptt) cc_final: 0.8876 (mptt) REVERT: H 82 LYS cc_start: 0.8319 (mttt) cc_final: 0.7817 (mmtt) REVERT: K 3828 LYS cc_start: 0.7796 (pttm) cc_final: 0.7546 (pttm) REVERT: K 3876 ASP cc_start: 0.8454 (m-30) cc_final: 0.7809 (p0) REVERT: N 226 ASP cc_start: 0.8292 (t0) cc_final: 0.7554 (t0) REVERT: N 320 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8704 (pt) REVERT: N 339 LEU cc_start: 0.8443 (pp) cc_final: 0.8175 (pp) REVERT: T 336 MET cc_start: 0.4254 (mmm) cc_final: 0.3347 (mmm) REVERT: T 500 MET cc_start: -0.0189 (ptm) cc_final: -0.1118 (ptm) REVERT: T 503 MET cc_start: 0.6151 (mmm) cc_final: 0.5635 (mpp) REVERT: R 72 TRP cc_start: 0.6273 (m100) cc_final: 0.5233 (m100) REVERT: R 140 GLN cc_start: 0.5685 (mt0) cc_final: 0.5177 (mm110) REVERT: R 228 TYR cc_start: 0.7220 (m-80) cc_final: 0.7018 (m-80) REVERT: R 230 LEU cc_start: 0.6250 (tp) cc_final: 0.5661 (tp) outliers start: 58 outliers final: 44 residues processed: 308 average time/residue: 0.3131 time to fit residues: 149.3223 Evaluate side-chains 298 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 250 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 92 ARG 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 58 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3898 HIS Chi-restraints excluded: chain K residue 3905 ILE 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 73 CYS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 73 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21716 Z= 0.280 Angle : 0.657 9.926 30585 Z= 0.365 Chirality : 0.042 0.208 3438 Planarity : 0.004 0.079 2870 Dihedral : 27.505 177.647 5203 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.39 % Allowed : 17.62 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.19), residues: 1830 helix: 1.51 (0.21), residues: 578 sheet: -2.14 (0.28), residues: 322 loop : -2.64 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 156 HIS 0.007 0.001 HIS R 44 PHE 0.013 0.001 PHE K3885 TYR 0.023 0.002 TYR N 13 ARG 0.008 0.000 ARG R 181 *********************** 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 337 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 267 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8301 (tm-30) REVERT: A 123 ASP cc_start: 0.8583 (m-30) cc_final: 0.8300 (m-30) REVERT: B 84 MET cc_start: 0.7906 (mmt) cc_final: 0.7659 (tpt) REVERT: C 56 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: D 48 ASP cc_start: 0.7026 (t0) cc_final: 0.6608 (t0) REVERT: D 54 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8991 (mmmt) REVERT: D 81 ASN cc_start: 0.8495 (m110) cc_final: 0.8275 (m110) REVERT: F 25 ASN cc_start: 0.8520 (t160) cc_final: 0.8240 (t0) REVERT: F 88 TYR cc_start: 0.8522 (m-10) cc_final: 0.7853 (m-10) REVERT: F 92 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8521 (ttp80) REVERT: G 18 SER cc_start: 0.8710 (OUTLIER) cc_final: 0.8015 (p) REVERT: H 30 ARG cc_start: 0.8399 (mpt180) cc_final: 0.7842 (mmp80) REVERT: H 40 LYS cc_start: 0.9134 (mptt) cc_final: 0.8928 (mptt) REVERT: H 76 ARG cc_start: 0.8685 (ttp-110) cc_final: 0.8448 (ttm170) REVERT: H 80 TYR cc_start: 0.7174 (m-80) cc_final: 0.6621 (m-80) REVERT: H 82 LYS cc_start: 0.8406 (mttt) cc_final: 0.8106 (mttm) REVERT: K 3777 MET cc_start: 0.3247 (mmp) cc_final: 0.2963 (mmp) REVERT: K 3828 LYS cc_start: 0.7827 (pttm) cc_final: 0.7625 (pttm) REVERT: K 3876 ASP cc_start: 0.8420 (m-30) cc_final: 0.7750 (p0) REVERT: N 226 ASP cc_start: 0.8261 (t0) cc_final: 0.7449 (t0) REVERT: N 256 LYS cc_start: 0.8550 (tppt) cc_final: 0.8325 (tppt) REVERT: N 320 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8816 (pt) REVERT: N 339 LEU cc_start: 0.8594 (pp) cc_final: 0.8301 (pp) REVERT: T 500 MET cc_start: -0.0222 (ptm) cc_final: -0.1160 (ptm) REVERT: T 503 MET cc_start: 0.6115 (mmm) cc_final: 0.5733 (mpp) REVERT: R 44 HIS cc_start: 0.3789 (OUTLIER) cc_final: 0.3392 (t-90) REVERT: R 53 PHE cc_start: 0.4718 (OUTLIER) cc_final: 0.3182 (m-80) REVERT: R 72 TRP cc_start: 0.6158 (m100) cc_final: 0.5153 (m100) REVERT: R 140 GLN cc_start: 0.5577 (mt0) cc_final: 0.4934 (mm110) REVERT: R 230 LEU cc_start: 0.6400 (tp) cc_final: 0.5786 (tp) outliers start: 70 outliers final: 48 residues processed: 311 average time/residue: 0.3212 time to fit residues: 152.9353 Evaluate side-chains 310 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 256 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 92 ARG 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 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain 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 3863 ILE Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain K residue 3946 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 127 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 157 optimal weight: 0.0670 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** K3867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 456 GLN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21716 Z= 0.172 Angle : 0.609 9.794 30585 Z= 0.338 Chirality : 0.040 0.210 3438 Planarity : 0.004 0.071 2870 Dihedral : 27.244 176.283 5203 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.95 % Allowed : 19.75 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.20), residues: 1830 helix: 1.94 (0.22), residues: 579 sheet: -1.93 (0.29), residues: 318 loop : -2.57 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 35 HIS 0.006 0.001 HIS K3898 PHE 0.015 0.001 PHE N 189 TYR 0.025 0.001 TYR N 115 ARG 0.007 0.000 ARG R 181 *********************** 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 326 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 279 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8376 (tm-30) REVERT: A 123 ASP cc_start: 0.8494 (m-30) cc_final: 0.8247 (m-30) REVERT: B 84 MET cc_start: 0.7874 (mmt) cc_final: 0.7648 (tpt) REVERT: C 56 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7128 (tp30) REVERT: D 30 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7077 (mtp85) REVERT: D 48 ASP cc_start: 0.6888 (t0) cc_final: 0.6488 (t0) REVERT: D 54 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8842 (mmmt) REVERT: D 59 MET cc_start: 0.9051 (mmm) cc_final: 0.8849 (mmm) REVERT: D 81 ASN cc_start: 0.8400 (m110) cc_final: 0.8111 (m110) REVERT: F 25 ASN cc_start: 0.8613 (t160) cc_final: 0.7841 (t0) REVERT: F 92 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8540 (ttp80) REVERT: G 18 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8010 (p) REVERT: G 92 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7211 (mm-30) REVERT: H 30 ARG cc_start: 0.8434 (mpt180) cc_final: 0.7889 (mmp-170) REVERT: H 82 LYS cc_start: 0.8282 (mttt) cc_final: 0.7851 (mmtt) REVERT: K 3777 MET cc_start: 0.2972 (mmp) cc_final: 0.2751 (mmp) REVERT: K 3828 LYS cc_start: 0.7654 (pttm) cc_final: 0.7444 (pttm) REVERT: K 3876 ASP cc_start: 0.8438 (m-30) cc_final: 0.7806 (p0) REVERT: K 3931 MET cc_start: 0.6670 (tpp) cc_final: 0.6381 (tpt) REVERT: N 256 LYS cc_start: 0.8526 (tppt) cc_final: 0.8295 (tppt) REVERT: N 320 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8742 (pt) REVERT: N 340 ASP cc_start: 0.8800 (t0) cc_final: 0.8117 (t0) REVERT: T 336 MET cc_start: 0.4368 (mmm) cc_final: 0.3492 (mmm) REVERT: T 500 MET cc_start: -0.0196 (ptm) cc_final: -0.1150 (ptm) REVERT: T 503 MET cc_start: 0.6139 (mmm) cc_final: 0.5731 (mpp) REVERT: R 44 HIS cc_start: 0.3652 (OUTLIER) cc_final: 0.3329 (t-90) REVERT: R 72 TRP cc_start: 0.5991 (m100) cc_final: 0.5014 (m100) REVERT: R 140 GLN cc_start: 0.5339 (mt0) cc_final: 0.4997 (mm110) REVERT: R 170 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.5164 (m170) REVERT: R 230 LEU cc_start: 0.6367 (tp) cc_final: 0.5789 (tp) outliers start: 47 outliers final: 34 residues processed: 309 average time/residue: 0.3365 time to fit residues: 159.0284 Evaluate side-chains 304 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 264 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 VAL 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 B residue 92 ARG Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 92 ARG 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 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3898 HIS Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain K residue 3946 PHE Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 316 VAL Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 176 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K3867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 21716 Z= 0.303 Angle : 0.686 10.525 30585 Z= 0.376 Chirality : 0.042 0.184 3438 Planarity : 0.004 0.083 2870 Dihedral : 27.433 177.646 5203 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.95 % Allowed : 19.25 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.19), residues: 1830 helix: 1.50 (0.21), residues: 576 sheet: -1.86 (0.28), residues: 316 loop : -2.62 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 156 HIS 0.010 0.001 HIS R 170 PHE 0.014 0.002 PHE K3885 TYR 0.026 0.002 TYR N 13 ARG 0.006 0.001 ARG R 181 *********************** 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 318 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 255 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8250 (tm-30) REVERT: A 123 ASP cc_start: 0.8484 (m-30) cc_final: 0.8250 (m-30) REVERT: C 56 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7280 (tp30) REVERT: D 48 ASP cc_start: 0.7001 (t0) cc_final: 0.6591 (t0) REVERT: D 54 LYS cc_start: 0.9207 (mmmt) cc_final: 0.8981 (mmmt) REVERT: D 81 ASN cc_start: 0.8553 (m110) cc_final: 0.8282 (m110) REVERT: E 133 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7483 (tt0) REVERT: F 25 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8198 (t0) REVERT: F 88 TYR cc_start: 0.8767 (m-10) cc_final: 0.8552 (m-10) REVERT: F 92 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8539 (ttp80) REVERT: G 18 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8019 (p) REVERT: G 84 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: G 104 GLN cc_start: 0.8666 (mp10) cc_final: 0.8260 (mp10) REVERT: H 30 ARG cc_start: 0.8401 (mpt180) cc_final: 0.7901 (mmp80) REVERT: H 82 LYS cc_start: 0.8489 (mttt) cc_final: 0.8184 (mttm) REVERT: K 3777 MET cc_start: 0.3099 (mmp) cc_final: 0.2768 (mmp) REVERT: K 3828 LYS cc_start: 0.7830 (pttm) cc_final: 0.7627 (pttm) REVERT: K 3867 GLN cc_start: 0.7766 (pm20) cc_final: 0.7388 (pm20) REVERT: K 3876 ASP cc_start: 0.8438 (m-30) cc_final: 0.7824 (p0) REVERT: K 3931 MET cc_start: 0.6803 (tpp) cc_final: 0.6450 (tpt) REVERT: N 256 LYS cc_start: 0.8510 (tppt) cc_final: 0.8278 (tppt) REVERT: N 320 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8826 (pt) REVERT: T 500 MET cc_start: -0.0219 (ptm) cc_final: -0.0427 (ptm) REVERT: R 72 TRP cc_start: 0.6087 (m100) cc_final: 0.5262 (m100) REVERT: R 140 GLN cc_start: 0.5553 (mt0) cc_final: 0.5087 (mm110) REVERT: R 230 LEU cc_start: 0.6440 (tp) cc_final: 0.5898 (tp) outliers start: 63 outliers final: 51 residues processed: 297 average time/residue: 0.2716 time to fit residues: 124.6483 Evaluate side-chains 307 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 250 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 71 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR 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 25 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain 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 3866 ILE Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3898 HIS Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain K residue 3946 PHE Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 128 MET Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 320 ILE Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 316 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 190 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: