Starting phenix.real_space_refine on Sat Apr 13 08:27:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiz_0695/04_2024/6kiz_0695_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiz_0695/04_2024/6kiz_0695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiz_0695/04_2024/6kiz_0695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiz_0695/04_2024/6kiz_0695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiz_0695/04_2024/6kiz_0695_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiz_0695/04_2024/6kiz_0695_updated.pdb" } resolution = 4.5 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= 0.002 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 8536 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 60 5.16 5 C 11641 2.51 5 N 3616 2.21 5 O 4281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 "K ARG 3916": "NH1" <-> "NH2" Residue "K ARG 3936": "NH1" <-> "NH2" Residue "K ARG 3965": "NH1" <-> "NH2" Residue "T TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19889 Number of models: 1 Model: "" Number of chains: 15 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: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} 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: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} 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: "N" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2759 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain breaks: 1 Chain: "K" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1436 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 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: "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: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16043 SG CYS K3957 92.948 68.835 21.393 1.00999.99 S ATOM 16057 SG CYS K3959 92.662 72.122 17.786 1.00999.99 S Time building chain proxies: 10.31, per 1000 atoms: 0.52 Number of scatterers: 19889 At special positions: 0 Unit cell: (146.3, 157.3, 140.8, 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 60 16.00 P 290 15.00 O 4281 8.00 N 3616 7.00 C 11641 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.70 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3957 " 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 21 sheets defined 29.3% alpha, 11.6% beta 140 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 10.10 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 4.276A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.610A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.622A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 72 removed outlier: 4.041A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 54 through 81 removed outlier: 3.722A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 119 removed outlier: 3.956A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 51 through 76 removed outlier: 3.691A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.868A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 removed outlier: 3.634A pdb=" N TYR H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 4.056A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'K' and resid 3816 through 3830 removed outlier: 3.520A pdb=" N LYS K3824 " --> pdb=" O PHE K3820 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS K3825 " --> pdb=" O ARG K3821 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS K3828 " --> pdb=" O LYS K3824 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU K3829 " --> pdb=" O LYS K3825 " (cutoff:3.500A) Processing helix chain 'K' and resid 3867 through 3878 Processing helix chain 'K' and resid 3901 through 3903 No H-bonds generated for 'chain 'K' and resid 3901 through 3903' Processing helix chain 'T' and resid 500 through 502 No H-bonds generated for 'chain 'T' and resid 500 through 502' Processing sheet with id= A, first strand: chain 'N' and resid 80 through 82 Processing sheet with id= B, first strand: chain 'N' and resid 122 through 126 Processing sheet with id= C, first strand: chain 'N' and resid 165 through 169 Processing sheet with id= D, first strand: chain 'N' and resid 243 through 246 removed outlier: 3.795A pdb=" N GLN N 243 " --> pdb=" O VAL N 224 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE N 221 " --> pdb=" O THR N 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR N 217 " --> pdb=" O ILE N 221 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'N' and resid 288 through 290 removed outlier: 4.206A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR N 277 " --> pdb=" O ALA N 268 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'N' and resid 300 through 303 Processing sheet with id= G, first strand: chain 'N' and resid 47 through 52 removed outlier: 5.170A pdb=" N ASP N 52 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE N 58 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 3833 through 3835 Processing sheet with id= I, first strand: chain 'K' and resid 3861 through 3864 Processing sheet with id= J, first strand: chain 'K' and resid 3913 through 3920 removed outlier: 3.853A pdb=" N VAL K3927 " --> pdb=" O ARG K3916 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE K3918 " --> pdb=" O HIS K3925 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS K3925 " --> pdb=" O ILE K3918 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE K3856 " --> pdb=" O ILE K3928 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA K3930 " --> pdb=" O MET K3854 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N MET K3854 " --> pdb=" O ALA K3930 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 110 through 115 removed outlier: 3.728A pdb=" N THR R 110 " --> pdb=" O SER R 106 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER R 106 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL R 103 " --> pdb=" O ALA R 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA R 94 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP R 92 " --> pdb=" O ALA R 105 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'R' and resid 154 through 157 removed outlier: 3.899A pdb=" N ARG R 154 " --> pdb=" O SER R 146 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL R 145 " --> pdb=" O ASN R 136 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN R 136 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'R' and resid 177 through 179 removed outlier: 3.778A pdb=" N HIS R 178 " --> pdb=" O VAL R 187 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'R' and resid 239 through 242 removed outlier: 3.537A pdb=" N LEU R 230 " --> pdb=" O LYS R 221 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS R 221 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA R 232 " --> pdb=" O PHE R 219 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE R 219 " --> pdb=" O ALA R 232 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'R' and resid 273 through 276 removed outlier: 3.712A pdb=" N LEU R 297 " --> pdb=" O VAL R 283 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'R' and resid 48 through 53 removed outlier: 6.769A pdb=" N SER R 63 " --> pdb=" O SER R 49 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL R 51 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA R 61 " --> pdb=" O VAL R 51 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'R' and resid 69 through 72 Processing sheet with id= R, first strand: chain 'R' and resid 195 through 198 removed outlier: 3.740A pdb=" N CYS R 195 " --> pdb=" O LEU R 209 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS R 207 " --> pdb=" O ILE R 197 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'R' and resid 304 through 309 removed outlier: 3.996A pdb=" N ILE R 305 " --> pdb=" O ALA R 319 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ALA R 319 " --> pdb=" O ILE R 305 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR R 307 " --> pdb=" O ALA R 317 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA R 317 " --> pdb=" O THR R 307 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'T' and resid 343 through 348 removed outlier: 3.532A pdb=" N SER T 473 " --> pdb=" O ARG T 343 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY T 345 " --> pdb=" O ALA T 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA T 471 " --> pdb=" O GLY T 345 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER T 347 " --> pdb=" O PHE T 469 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'T' and resid 372 through 374 437 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 361 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 8.58 Time building geometry restraints manager: 10.34 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: 4279 1.33 - 1.45: 5959 1.45 - 1.57: 9973 1.57 - 1.69: 578 1.69 - 1.81: 87 Bond restraints: 20876 Sorted by residual: bond pdb=" C SER N 108 " pdb=" N PRO N 109 " ideal model delta sigma weight residual 1.335 1.360 -0.025 8.70e-03 1.32e+04 8.27e+00 bond pdb=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.19e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.350 -0.051 2.00e-02 2.50e+03 6.38e+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 5.68e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.08e+00 ... (remaining 20871 not shown) Histogram of bond angle deviations from ideal: 89.47 - 98.52: 7 98.52 - 107.57: 2862 107.57 - 116.63: 13250 116.63 - 125.68: 12235 125.68 - 134.73: 1103 Bond angle restraints: 29457 Sorted by residual: angle pdb=" C GLN N 323 " pdb=" N ASN N 324 " pdb=" CA ASN N 324 " ideal model delta sigma weight residual 124.82 134.73 -9.91 1.78e+00 3.16e-01 3.10e+01 angle pdb=" N VAL G 27 " pdb=" CA VAL G 27 " pdb=" C VAL G 27 " ideal model delta sigma weight residual 112.96 108.43 4.53 1.00e+00 1.00e+00 2.05e+01 angle pdb=" C ASP B 24 " pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 124.82 132.47 -7.65 1.78e+00 3.16e-01 1.85e+01 angle pdb=" CG SAH K4001 " pdb=" SD SAH K4001 " pdb=" C5' SAH K4001 " ideal model delta sigma weight residual 101.77 89.47 12.30 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 125.50 -5.30 1.50e+00 4.44e-01 1.25e+01 ... (remaining 29452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 10220 34.36 - 68.71: 1487 68.71 - 103.07: 39 103.07 - 137.42: 1 137.42 - 171.78: 3 Dihedral angle restraints: 11750 sinusoidal: 6646 harmonic: 5104 Sorted by residual: dihedral pdb=" CA GLY N 194 " pdb=" C GLY N 194 " pdb=" N THR N 195 " pdb=" CA THR N 195 " ideal model delta harmonic sigma weight residual -180.00 -138.83 -41.17 0 5.00e+00 4.00e-02 6.78e+01 dihedral pdb=" CA GLU N 16 " pdb=" C GLU N 16 " pdb=" N ALA N 17 " pdb=" CA ALA N 17 " ideal model delta harmonic sigma weight residual -180.00 -152.68 -27.32 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -153.93 -26.07 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 11747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2133 0.042 - 0.083: 829 0.083 - 0.125: 271 0.125 - 0.166: 66 0.166 - 0.208: 8 Chirality restraints: 3307 Sorted by residual: chirality pdb=" CB ILE T 482 " pdb=" CA ILE T 482 " pdb=" CG1 ILE T 482 " pdb=" CG2 ILE T 482 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1' SAH K4001 " pdb=" C2' SAH K4001 " pdb=" N9 SAH K4001 " pdb=" O4' SAH K4001 " both_signs ideal model delta sigma weight residual False 2.35 2.53 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.24e-01 ... (remaining 3304 not shown) Planarity restraints: 2724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " 0.036 2.00e-02 2.50e+03 1.54e-02 7.12e+00 pdb=" N9 DG I 121 " -0.034 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 100 " -0.034 2.00e-02 2.50e+03 1.45e-02 6.28e+00 pdb=" N9 DG I 100 " 0.033 2.00e-02 2.50e+03 pdb=" C8 DG I 100 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 100 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG I 100 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 100 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 100 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DG I 100 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DG I 100 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 100 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 100 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DG I 100 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER N 108 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO N 109 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO N 109 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO N 109 " -0.034 5.00e-02 4.00e+02 ... (remaining 2721 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4068 2.78 - 3.31: 17080 3.31 - 3.84: 37195 3.84 - 4.37: 41724 4.37 - 4.90: 63319 Nonbonded interactions: 163386 Sorted by model distance: nonbonded pdb=" OG SER N 91 " pdb=" O GLN N 102 " model vdw 2.253 2.440 nonbonded pdb=" N CYS K3959 " pdb="ZN ZN K4002 " model vdw 2.254 2.310 nonbonded pdb=" OG1 THR N 217 " pdb=" OD1 ASP N 219 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.267 2.440 nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.277 2.520 ... (remaining 163381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 5.350 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 66.270 Find NCS groups from input model: 0.690 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: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 0.075 20876 Z= 0.430 Angle : 0.857 12.302 29457 Z= 0.492 Chirality : 0.050 0.208 3307 Planarity : 0.006 0.060 2724 Dihedral : 23.337 171.777 8460 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.09 (0.17), residues: 1729 helix: -0.37 (0.19), residues: 547 sheet: -2.98 (0.33), residues: 194 loop : -2.98 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP T 366 HIS 0.010 0.002 HIS F 75 PHE 0.027 0.002 PHE E 104 TYR 0.038 0.003 TYR B 88 ARG 0.011 0.001 ARG N 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8708 (mt-10) REVERT: A 64 LYS cc_start: 0.9372 (mtmm) cc_final: 0.9017 (mtmm) REVERT: A 68 GLN cc_start: 0.9038 (tt0) cc_final: 0.8804 (pt0) REVERT: A 76 GLN cc_start: 0.9116 (tt0) cc_final: 0.8856 (pt0) REVERT: A 90 MET cc_start: 0.9171 (mmt) cc_final: 0.8886 (mmp) REVERT: A 94 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8846 (mm-30) REVERT: A 125 GLN cc_start: 0.9373 (mt0) cc_final: 0.9121 (mt0) REVERT: B 63 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8711 (mt-10) REVERT: B 84 MET cc_start: 0.8852 (mmm) cc_final: 0.8370 (mmm) REVERT: C 56 GLU cc_start: 0.9031 (tt0) cc_final: 0.8736 (tt0) REVERT: C 64 GLU cc_start: 0.9002 (tp30) cc_final: 0.8627 (tp30) REVERT: C 75 LYS cc_start: 0.9597 (mmtp) cc_final: 0.8918 (mmmm) REVERT: C 90 ASP cc_start: 0.8844 (t0) cc_final: 0.8520 (t70) REVERT: C 101 THR cc_start: 0.9061 (m) cc_final: 0.8565 (p) REVERT: C 110 ASN cc_start: 0.9180 (t0) cc_final: 0.8541 (m-40) REVERT: D 73 GLU cc_start: 0.9348 (tp30) cc_final: 0.9036 (tp30) REVERT: D 90 GLU cc_start: 0.8562 (mp0) cc_final: 0.8358 (mp0) REVERT: E 64 LYS cc_start: 0.9371 (mtmm) cc_final: 0.8982 (mtmm) REVERT: E 90 MET cc_start: 0.9179 (mmt) cc_final: 0.8750 (mmp) REVERT: E 125 GLN cc_start: 0.9399 (mt0) cc_final: 0.8935 (mp10) REVERT: F 44 LYS cc_start: 0.9284 (tptm) cc_final: 0.9029 (tppp) REVERT: F 49 LEU cc_start: 0.9693 (mt) cc_final: 0.9438 (mm) REVERT: F 59 LYS cc_start: 0.9048 (tttp) cc_final: 0.8708 (ttpp) REVERT: F 63 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8634 (mt-10) REVERT: F 84 MET cc_start: 0.8918 (mmm) cc_final: 0.8346 (tpp) REVERT: G 56 GLU cc_start: 0.9086 (tt0) cc_final: 0.8702 (tt0) REVERT: G 61 GLU cc_start: 0.9240 (tp30) cc_final: 0.8922 (tp30) REVERT: G 90 ASP cc_start: 0.8833 (t0) cc_final: 0.8531 (t70) REVERT: G 92 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8517 (mt-10) REVERT: G 101 THR cc_start: 0.8787 (m) cc_final: 0.8366 (p) REVERT: H 80 TYR cc_start: 0.8635 (m-10) cc_final: 0.7937 (m-10) REVERT: H 83 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.8165 (mtp-110) REVERT: N 128 MET cc_start: 0.9073 (tpt) cc_final: 0.8604 (tpt) REVERT: N 197 ASN cc_start: 0.8222 (t0) cc_final: 0.7974 (t0) REVERT: N 243 GLN cc_start: 0.9476 (tp-100) cc_final: 0.8988 (tm-30) REVERT: N 256 LYS cc_start: 0.9299 (tptm) cc_final: 0.9083 (mmmt) REVERT: K 3884 MET cc_start: 0.5800 (mtt) cc_final: 0.5554 (mtt) REVERT: K 3927 VAL cc_start: 0.2113 (t) cc_final: 0.1780 (m) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.4951 time to fit residues: 216.3000 Evaluate side-chains 187 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 40.0000 chunk 150 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 179 optimal weight: 50.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS C 31 HIS C 104 GLN D 46 HIS E 39 HIS E 68 GLN F 25 ASN G 31 HIS G 89 ASN N 12 ASN N 79 HIS ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 320 HIS T 354 GLN T 381 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20876 Z= 0.349 Angle : 0.655 6.804 29457 Z= 0.376 Chirality : 0.042 0.181 3307 Planarity : 0.005 0.041 2724 Dihedral : 28.288 168.414 5095 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.95 (0.19), residues: 1729 helix: 1.39 (0.22), residues: 548 sheet: -2.71 (0.32), residues: 231 loop : -2.71 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 95 HIS 0.014 0.002 HIS R 178 PHE 0.010 0.001 PHE N 104 TYR 0.022 0.002 TYR K3874 ARG 0.008 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8789 (mt-10) REVERT: A 64 LYS cc_start: 0.9410 (mtmm) cc_final: 0.9061 (mtmm) REVERT: A 76 GLN cc_start: 0.9116 (tt0) cc_final: 0.8899 (pt0) REVERT: A 90 MET cc_start: 0.9335 (mmt) cc_final: 0.9038 (mmp) REVERT: A 94 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8799 (mm-30) REVERT: B 25 ASN cc_start: 0.8884 (m110) cc_final: 0.8492 (m110) REVERT: B 63 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8715 (mt-10) REVERT: B 84 MET cc_start: 0.8898 (mmm) cc_final: 0.8355 (mmm) REVERT: C 56 GLU cc_start: 0.9081 (tt0) cc_final: 0.8769 (tt0) REVERT: C 61 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8740 (tm-30) REVERT: C 64 GLU cc_start: 0.9056 (tp30) cc_final: 0.8761 (tp30) REVERT: C 75 LYS cc_start: 0.9632 (mmtp) cc_final: 0.9016 (mmmm) REVERT: C 90 ASP cc_start: 0.8856 (t0) cc_final: 0.8543 (t70) REVERT: C 110 ASN cc_start: 0.9219 (t0) cc_final: 0.8597 (m-40) REVERT: D 27 ARG cc_start: 0.7144 (tmt170) cc_final: 0.6830 (tmt170) REVERT: D 76 ARG cc_start: 0.9339 (ttm110) cc_final: 0.9009 (ttp-110) REVERT: D 90 GLU cc_start: 0.8392 (mp0) cc_final: 0.8142 (mp0) REVERT: E 89 VAL cc_start: 0.9289 (t) cc_final: 0.9026 (p) REVERT: E 106 ASP cc_start: 0.8719 (m-30) cc_final: 0.8503 (m-30) REVERT: E 125 GLN cc_start: 0.9365 (mt0) cc_final: 0.9106 (mp10) REVERT: F 44 LYS cc_start: 0.9312 (tptm) cc_final: 0.9017 (tppp) REVERT: F 49 LEU cc_start: 0.9584 (mt) cc_final: 0.9163 (mm) REVERT: F 84 MET cc_start: 0.8927 (mmm) cc_final: 0.8132 (tpp) REVERT: G 56 GLU cc_start: 0.9023 (tt0) cc_final: 0.8559 (tt0) REVERT: G 61 GLU cc_start: 0.9210 (tp30) cc_final: 0.8886 (tp30) REVERT: G 73 ASN cc_start: 0.9524 (t0) cc_final: 0.9310 (t0) REVERT: G 90 ASP cc_start: 0.8813 (t0) cc_final: 0.8391 (t70) REVERT: G 101 THR cc_start: 0.8847 (m) cc_final: 0.8383 (p) REVERT: N 167 TYR cc_start: 0.8982 (m-10) cc_final: 0.8489 (m-80) REVERT: N 246 GLN cc_start: 0.8874 (pm20) cc_final: 0.8569 (pm20) REVERT: K 3816 MET cc_start: 0.5497 (ttt) cc_final: 0.4344 (mmm) REVERT: K 3868 THR cc_start: 0.4567 (p) cc_final: 0.4137 (p) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.3760 time to fit residues: 120.0666 Evaluate side-chains 174 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 194 optimal weight: 40.0000 chunk 160 optimal weight: 8.9990 chunk 178 optimal weight: 30.0000 chunk 61 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 46 HIS F 25 ASN N 12 ASN ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 20876 Z= 0.394 Angle : 0.659 7.910 29457 Z= 0.375 Chirality : 0.042 0.151 3307 Planarity : 0.004 0.060 2724 Dihedral : 28.134 165.916 5095 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.07 % Allowed : 2.73 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.72 (0.20), residues: 1729 helix: 1.53 (0.22), residues: 547 sheet: -2.51 (0.32), residues: 226 loop : -2.54 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 366 HIS 0.009 0.002 HIS F 75 PHE 0.011 0.001 PHE K3844 TYR 0.017 0.002 TYR K3874 ARG 0.006 0.001 ARG T 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8852 (mt-10) REVERT: A 90 MET cc_start: 0.9403 (mmt) cc_final: 0.9117 (mmm) REVERT: A 94 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8857 (mm-30) REVERT: B 25 ASN cc_start: 0.8802 (m110) cc_final: 0.8440 (m110) REVERT: B 44 LYS cc_start: 0.8768 (tttt) cc_final: 0.8535 (tttt) REVERT: B 63 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8978 (mt-10) REVERT: B 84 MET cc_start: 0.8951 (mmm) cc_final: 0.8357 (mmm) REVERT: C 61 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8787 (tm-30) REVERT: C 64 GLU cc_start: 0.9018 (tp30) cc_final: 0.8789 (tp30) REVERT: C 90 ASP cc_start: 0.8900 (t0) cc_final: 0.8642 (t70) REVERT: D 27 ARG cc_start: 0.7022 (tmt170) cc_final: 0.6551 (tmt170) REVERT: D 44 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8845 (tm-30) REVERT: D 90 GLU cc_start: 0.8405 (mp0) cc_final: 0.8151 (mp0) REVERT: E 106 ASP cc_start: 0.8759 (m-30) cc_final: 0.8510 (m-30) REVERT: E 125 GLN cc_start: 0.9358 (mt0) cc_final: 0.9137 (mp10) REVERT: F 44 LYS cc_start: 0.9379 (tptm) cc_final: 0.9155 (tppp) REVERT: F 49 LEU cc_start: 0.9418 (mt) cc_final: 0.9091 (mm) REVERT: F 53 GLU cc_start: 0.9278 (mp0) cc_final: 0.9026 (mp0) REVERT: F 84 MET cc_start: 0.8904 (mmm) cc_final: 0.7956 (tpp) REVERT: G 56 GLU cc_start: 0.8945 (tt0) cc_final: 0.8494 (tt0) REVERT: G 61 GLU cc_start: 0.9235 (tp30) cc_final: 0.8987 (tm-30) REVERT: G 73 ASN cc_start: 0.9551 (t0) cc_final: 0.9342 (t0) REVERT: G 90 ASP cc_start: 0.8920 (t0) cc_final: 0.7730 (t0) REVERT: G 93 LEU cc_start: 0.9501 (mm) cc_final: 0.9041 (mt) REVERT: G 101 THR cc_start: 0.9043 (m) cc_final: 0.8704 (p) REVERT: N 167 TYR cc_start: 0.9027 (m-10) cc_final: 0.8564 (m-80) REVERT: N 243 GLN cc_start: 0.9561 (mm-40) cc_final: 0.9260 (mm110) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.4065 time to fit residues: 123.9777 Evaluate side-chains 161 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 10.0000 chunk 135 optimal weight: 50.0000 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 171 optimal weight: 30.0000 chunk 51 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 46 HIS F 25 ASN N 12 ASN ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 20876 Z= 0.316 Angle : 0.613 9.448 29457 Z= 0.351 Chirality : 0.040 0.149 3307 Planarity : 0.004 0.034 2724 Dihedral : 28.039 167.523 5095 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.56 (0.20), residues: 1729 helix: 1.80 (0.22), residues: 542 sheet: -2.60 (0.31), residues: 238 loop : -2.45 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 327 HIS 0.007 0.001 HIS F 75 PHE 0.009 0.001 PHE T 464 TYR 0.015 0.002 TYR K3935 ARG 0.006 0.000 ARG T 367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9122 (t) cc_final: 0.8865 (t) REVERT: A 50 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8810 (mt-10) REVERT: A 90 MET cc_start: 0.9387 (mmt) cc_final: 0.9017 (mmm) REVERT: A 94 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8764 (mm-30) REVERT: B 25 ASN cc_start: 0.8839 (m110) cc_final: 0.8485 (m110) REVERT: B 44 LYS cc_start: 0.8791 (tttt) cc_final: 0.8530 (tttt) REVERT: B 59 LYS cc_start: 0.9359 (ttpp) cc_final: 0.9148 (ttpp) REVERT: B 63 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8767 (mt-10) REVERT: B 84 MET cc_start: 0.8861 (mmm) cc_final: 0.8294 (mmm) REVERT: C 56 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8966 (tm-30) REVERT: C 61 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8800 (tm-30) REVERT: C 64 GLU cc_start: 0.8960 (tp30) cc_final: 0.8730 (tp30) REVERT: C 90 ASP cc_start: 0.8923 (t0) cc_final: 0.8588 (t70) REVERT: D 27 ARG cc_start: 0.6888 (tmt170) cc_final: 0.6425 (tmt170) REVERT: D 44 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8908 (tm-30) REVERT: D 90 GLU cc_start: 0.8413 (mp0) cc_final: 0.8159 (mp0) REVERT: E 106 ASP cc_start: 0.8739 (m-30) cc_final: 0.8494 (m-30) REVERT: E 120 MET cc_start: 0.8837 (tpt) cc_final: 0.8501 (mtp) REVERT: E 125 GLN cc_start: 0.9343 (mt0) cc_final: 0.9140 (mp10) REVERT: F 44 LYS cc_start: 0.9387 (tptm) cc_final: 0.9131 (tppp) REVERT: F 49 LEU cc_start: 0.9443 (mt) cc_final: 0.8931 (mm) REVERT: F 53 GLU cc_start: 0.9228 (mp0) cc_final: 0.8783 (mp0) REVERT: F 84 MET cc_start: 0.8827 (mmm) cc_final: 0.7850 (tpp) REVERT: G 56 GLU cc_start: 0.8898 (tt0) cc_final: 0.8407 (tt0) REVERT: G 75 LYS cc_start: 0.9594 (mmtt) cc_final: 0.9210 (mmmm) REVERT: G 90 ASP cc_start: 0.8465 (t0) cc_final: 0.8032 (t0) REVERT: G 93 LEU cc_start: 0.9501 (mm) cc_final: 0.9061 (mt) REVERT: G 101 THR cc_start: 0.9027 (m) cc_final: 0.8648 (p) REVERT: N 167 TYR cc_start: 0.9066 (m-10) cc_final: 0.8596 (m-80) REVERT: N 243 GLN cc_start: 0.9544 (mm-40) cc_final: 0.9231 (mm110) REVERT: K 3816 MET cc_start: 0.5536 (ttt) cc_final: 0.4881 (mtp) REVERT: T 315 MET cc_start: -0.0668 (mmp) cc_final: -0.1450 (mmt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.3883 time to fit residues: 116.4093 Evaluate side-chains 162 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 30.0000 chunk 108 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 142 optimal weight: 40.0000 chunk 78 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 171 optimal weight: 50.0000 chunk 48 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS F 25 ASN N 12 ASN ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20876 Z= 0.247 Angle : 0.575 8.622 29457 Z= 0.331 Chirality : 0.039 0.157 3307 Planarity : 0.004 0.039 2724 Dihedral : 27.903 170.298 5095 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.32 (0.20), residues: 1729 helix: 2.17 (0.22), residues: 539 sheet: -2.52 (0.31), residues: 240 loop : -2.39 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 327 HIS 0.006 0.001 HIS F 75 PHE 0.008 0.001 PHE K3778 TYR 0.016 0.001 TYR D 80 ARG 0.005 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9041 (t) cc_final: 0.8791 (t) REVERT: A 50 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8818 (mt-10) REVERT: A 90 MET cc_start: 0.9374 (mmt) cc_final: 0.8953 (mmm) REVERT: A 94 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8766 (mm-30) REVERT: A 97 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8372 (mt-10) REVERT: B 25 ASN cc_start: 0.8753 (m110) cc_final: 0.8303 (m110) REVERT: B 44 LYS cc_start: 0.8798 (tttt) cc_final: 0.8564 (tttt) REVERT: B 84 MET cc_start: 0.8834 (mmm) cc_final: 0.8350 (mmm) REVERT: C 56 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8976 (tm-30) REVERT: C 61 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8750 (tm-30) REVERT: C 64 GLU cc_start: 0.8946 (tp30) cc_final: 0.8729 (tp30) REVERT: C 90 ASP cc_start: 0.8917 (t0) cc_final: 0.8574 (t70) REVERT: D 27 ARG cc_start: 0.6787 (tmt170) cc_final: 0.6363 (tmt170) REVERT: D 90 GLU cc_start: 0.8533 (mp0) cc_final: 0.8286 (mp0) REVERT: E 54 TYR cc_start: 0.8840 (m-80) cc_final: 0.8536 (m-10) REVERT: E 106 ASP cc_start: 0.8683 (m-30) cc_final: 0.8451 (m-30) REVERT: F 44 LYS cc_start: 0.9397 (tptm) cc_final: 0.9114 (tppp) REVERT: F 49 LEU cc_start: 0.9388 (mt) cc_final: 0.9119 (mm) REVERT: F 53 GLU cc_start: 0.9240 (mp0) cc_final: 0.9030 (mp0) REVERT: F 84 MET cc_start: 0.8829 (mmm) cc_final: 0.8438 (tpp) REVERT: G 56 GLU cc_start: 0.8884 (tt0) cc_final: 0.8384 (tt0) REVERT: G 73 ASN cc_start: 0.9475 (t0) cc_final: 0.9246 (t0) REVERT: G 75 LYS cc_start: 0.9587 (mmtt) cc_final: 0.9204 (mmmm) REVERT: G 101 THR cc_start: 0.9004 (m) cc_final: 0.8624 (p) REVERT: N 167 TYR cc_start: 0.9088 (m-10) cc_final: 0.8652 (m-80) REVERT: N 243 GLN cc_start: 0.9502 (mm-40) cc_final: 0.9200 (mm110) REVERT: T 315 MET cc_start: -0.0614 (mmp) cc_final: -0.1300 (mmt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.3753 time to fit residues: 113.4788 Evaluate side-chains 169 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.0980 chunk 172 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 chunk 159 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 30.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS F 25 ASN N 12 ASN K3906 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20876 Z= 0.156 Angle : 0.536 8.735 29457 Z= 0.309 Chirality : 0.038 0.147 3307 Planarity : 0.003 0.046 2724 Dihedral : 27.705 174.181 5095 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.99 (0.21), residues: 1729 helix: 2.58 (0.22), residues: 542 sheet: -2.34 (0.32), residues: 238 loop : -2.29 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP T 327 HIS 0.006 0.001 HIS R 178 PHE 0.008 0.001 PHE K3778 TYR 0.020 0.001 TYR K3935 ARG 0.003 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8921 (t) cc_final: 0.8667 (t) REVERT: A 50 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8779 (mt-10) REVERT: A 90 MET cc_start: 0.9298 (mmt) cc_final: 0.8990 (mmm) REVERT: A 94 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8740 (mm-30) REVERT: A 97 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8333 (mt-10) REVERT: A 105 GLU cc_start: 0.9024 (tp30) cc_final: 0.8774 (tp30) REVERT: A 120 MET cc_start: 0.8235 (mtt) cc_final: 0.7932 (mtt) REVERT: B 25 ASN cc_start: 0.8595 (m110) cc_final: 0.8198 (m110) REVERT: B 68 ASP cc_start: 0.8880 (m-30) cc_final: 0.8676 (m-30) REVERT: B 84 MET cc_start: 0.8776 (mmm) cc_final: 0.8345 (mmm) REVERT: C 61 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8678 (tm-30) REVERT: C 90 ASP cc_start: 0.8842 (t0) cc_final: 0.8511 (t70) REVERT: C 110 ASN cc_start: 0.9131 (t0) cc_final: 0.8627 (m-40) REVERT: D 27 ARG cc_start: 0.6554 (tmt170) cc_final: 0.6062 (tmt170) REVERT: D 90 GLU cc_start: 0.8608 (mp0) cc_final: 0.8308 (mp0) REVERT: E 54 TYR cc_start: 0.8816 (m-80) cc_final: 0.8322 (m-10) REVERT: E 106 ASP cc_start: 0.8613 (m-30) cc_final: 0.8252 (m-30) REVERT: E 120 MET cc_start: 0.8846 (tpt) cc_final: 0.8641 (mmm) REVERT: E 125 GLN cc_start: 0.9086 (mp10) cc_final: 0.8708 (mp10) REVERT: F 44 LYS cc_start: 0.9361 (tptm) cc_final: 0.9054 (tppp) REVERT: F 49 LEU cc_start: 0.9624 (mt) cc_final: 0.9143 (mm) REVERT: F 53 GLU cc_start: 0.9330 (mp0) cc_final: 0.9058 (mp0) REVERT: F 84 MET cc_start: 0.8828 (mmm) cc_final: 0.8464 (tpp) REVERT: G 73 ASN cc_start: 0.9489 (t0) cc_final: 0.9263 (t0) REVERT: G 75 LYS cc_start: 0.9568 (mmtt) cc_final: 0.9198 (mmmm) REVERT: G 90 ASP cc_start: 0.8485 (t0) cc_final: 0.8037 (t70) REVERT: G 101 THR cc_start: 0.8873 (m) cc_final: 0.8421 (p) REVERT: N 167 TYR cc_start: 0.9094 (m-10) cc_final: 0.8771 (m-80) REVERT: N 197 ASN cc_start: 0.7940 (t0) cc_final: 0.7691 (t0) REVERT: N 243 GLN cc_start: 0.9526 (mm-40) cc_final: 0.9220 (mm110) REVERT: R 198 TRP cc_start: 0.5617 (m100) cc_final: 0.5310 (m-10) REVERT: T 315 MET cc_start: -0.0521 (mmp) cc_final: -0.1280 (mmt) REVERT: T 336 MET cc_start: 0.5546 (ttm) cc_final: 0.4915 (tpp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.3605 time to fit residues: 120.0009 Evaluate side-chains 175 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.0570 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 overall best weight: 6.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 68 ASN F 25 ASN N 12 ASN ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 20876 Z= 0.390 Angle : 0.640 8.401 29457 Z= 0.363 Chirality : 0.041 0.146 3307 Planarity : 0.004 0.045 2724 Dihedral : 27.811 168.216 5095 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.31 (0.20), residues: 1729 helix: 2.00 (0.22), residues: 547 sheet: -2.34 (0.31), residues: 238 loop : -2.36 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP T 327 HIS 0.008 0.002 HIS F 75 PHE 0.010 0.001 PHE N 159 TYR 0.013 0.002 TYR A 54 ARG 0.007 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9032 (t) cc_final: 0.8775 (t) REVERT: A 50 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8823 (mt-10) REVERT: A 90 MET cc_start: 0.9430 (mmt) cc_final: 0.9054 (mmm) REVERT: A 94 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8845 (mm-30) REVERT: A 97 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8283 (mt-10) REVERT: A 105 GLU cc_start: 0.8878 (tp30) cc_final: 0.8677 (tp30) REVERT: B 25 ASN cc_start: 0.8621 (m110) cc_final: 0.8188 (m110) REVERT: B 59 LYS cc_start: 0.9377 (ttpp) cc_final: 0.9115 (ttpp) REVERT: B 63 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8732 (mt-10) REVERT: B 84 MET cc_start: 0.8969 (mmm) cc_final: 0.8460 (mmm) REVERT: C 61 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8812 (tm-30) REVERT: C 64 GLU cc_start: 0.9159 (tp30) cc_final: 0.8805 (tp30) REVERT: C 90 ASP cc_start: 0.8922 (t0) cc_final: 0.8610 (t70) REVERT: D 27 ARG cc_start: 0.6785 (tmt170) cc_final: 0.6345 (tmt170) REVERT: D 90 GLU cc_start: 0.8500 (mp0) cc_final: 0.8284 (mp0) REVERT: E 50 GLU cc_start: 0.9169 (tt0) cc_final: 0.8922 (tt0) REVERT: E 54 TYR cc_start: 0.8945 (m-80) cc_final: 0.8565 (m-10) REVERT: E 106 ASP cc_start: 0.8724 (m-30) cc_final: 0.8505 (m-30) REVERT: F 44 LYS cc_start: 0.9409 (tptm) cc_final: 0.9164 (tppp) REVERT: F 49 LEU cc_start: 0.9644 (mt) cc_final: 0.9348 (mm) REVERT: F 84 MET cc_start: 0.8912 (mmm) cc_final: 0.8041 (tpp) REVERT: G 64 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8816 (tm-30) REVERT: G 90 ASP cc_start: 0.8531 (t0) cc_final: 0.8092 (t0) REVERT: G 93 LEU cc_start: 0.9483 (mm) cc_final: 0.9135 (mm) REVERT: G 101 THR cc_start: 0.8950 (m) cc_final: 0.8475 (p) REVERT: N 167 TYR cc_start: 0.9105 (m-10) cc_final: 0.8727 (m-80) REVERT: N 276 LEU cc_start: 0.9150 (mp) cc_final: 0.8666 (mt) REVERT: K 3816 MET cc_start: 0.5319 (ttt) cc_final: 0.4598 (mmm) REVERT: T 315 MET cc_start: -0.0948 (mmp) cc_final: -0.1560 (mmt) REVERT: T 500 MET cc_start: 0.5102 (mtt) cc_final: 0.4632 (mtt) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3851 time to fit residues: 107.2587 Evaluate side-chains 149 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN N 12 ASN ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3906 ASN K3907 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20876 Z= 0.254 Angle : 0.579 8.167 29457 Z= 0.332 Chirality : 0.039 0.143 3307 Planarity : 0.004 0.046 2724 Dihedral : 27.744 170.089 5095 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.20 (0.20), residues: 1729 helix: 2.12 (0.22), residues: 551 sheet: -2.39 (0.31), residues: 248 loop : -2.28 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 327 HIS 0.006 0.001 HIS R 178 PHE 0.012 0.001 PHE C 25 TYR 0.011 0.001 TYR K3942 ARG 0.004 0.000 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9025 (t) cc_final: 0.8790 (t) REVERT: A 50 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8765 (mt-10) REVERT: A 90 MET cc_start: 0.9382 (mmt) cc_final: 0.8965 (mmm) REVERT: A 94 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8756 (mm-30) REVERT: A 97 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8354 (mt-10) REVERT: B 25 ASN cc_start: 0.8550 (m110) cc_final: 0.8162 (m110) REVERT: B 84 MET cc_start: 0.8861 (mmm) cc_final: 0.8370 (mmm) REVERT: C 61 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8744 (tm-30) REVERT: C 64 GLU cc_start: 0.9170 (tp30) cc_final: 0.8809 (tp30) REVERT: C 90 ASP cc_start: 0.8862 (t0) cc_final: 0.8562 (t70) REVERT: D 27 ARG cc_start: 0.6570 (tmt170) cc_final: 0.6114 (tmt170) REVERT: D 90 GLU cc_start: 0.8518 (mp0) cc_final: 0.8298 (mp0) REVERT: E 50 GLU cc_start: 0.9171 (tt0) cc_final: 0.8921 (tt0) REVERT: E 54 TYR cc_start: 0.8850 (m-80) cc_final: 0.8451 (m-10) REVERT: E 106 ASP cc_start: 0.8691 (m-30) cc_final: 0.8473 (m-30) REVERT: F 44 LYS cc_start: 0.9392 (tptm) cc_final: 0.9107 (tppp) REVERT: F 49 LEU cc_start: 0.9389 (mt) cc_final: 0.9176 (mm) REVERT: F 84 MET cc_start: 0.8834 (mmm) cc_final: 0.7935 (tpp) REVERT: G 61 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8669 (tm-30) REVERT: G 64 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8873 (tm-30) REVERT: G 75 LYS cc_start: 0.9562 (mmtt) cc_final: 0.9227 (mmmt) REVERT: G 90 ASP cc_start: 0.8467 (t0) cc_final: 0.8153 (t70) REVERT: G 93 LEU cc_start: 0.9499 (mm) cc_final: 0.9255 (mt) REVERT: G 101 THR cc_start: 0.8979 (m) cc_final: 0.8567 (p) REVERT: N 167 TYR cc_start: 0.9108 (m-10) cc_final: 0.8745 (m-80) REVERT: N 276 LEU cc_start: 0.9249 (mp) cc_final: 0.8816 (mt) REVERT: K 3816 MET cc_start: 0.5304 (ttt) cc_final: 0.4593 (mmm) REVERT: R 241 TRP cc_start: 0.8231 (m100) cc_final: 0.8018 (m100) REVERT: T 315 MET cc_start: -0.0779 (mmp) cc_final: -0.1434 (mmt) REVERT: T 500 MET cc_start: 0.5636 (mtt) cc_final: 0.5176 (mtt) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.3805 time to fit residues: 110.1481 Evaluate side-chains 156 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 40.0000 chunk 182 optimal weight: 0.2980 chunk 166 optimal weight: 50.0000 chunk 177 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 139 optimal weight: 40.0000 chunk 54 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 116 optimal weight: 30.0000 overall best weight: 5.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 25 ASN N 12 ASN ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20876 Z= 0.355 Angle : 0.627 9.164 29457 Z= 0.357 Chirality : 0.041 0.143 3307 Planarity : 0.004 0.047 2724 Dihedral : 27.777 168.560 5095 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.28 (0.20), residues: 1729 helix: 1.93 (0.22), residues: 551 sheet: -2.43 (0.31), residues: 248 loop : -2.25 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 95 HIS 0.014 0.002 HIS R 178 PHE 0.011 0.001 PHE K3844 TYR 0.025 0.002 TYR D 80 ARG 0.009 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9034 (t) cc_final: 0.8762 (t) REVERT: A 50 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8788 (mt-10) REVERT: A 90 MET cc_start: 0.9425 (mmt) cc_final: 0.9039 (mmm) REVERT: A 94 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8806 (mm-30) REVERT: A 97 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8341 (mt-10) REVERT: B 25 ASN cc_start: 0.8614 (m110) cc_final: 0.8239 (m110) REVERT: B 63 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8672 (mt-10) REVERT: B 84 MET cc_start: 0.8920 (mmm) cc_final: 0.8365 (mmm) REVERT: C 61 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8770 (tm-30) REVERT: C 64 GLU cc_start: 0.9183 (tp30) cc_final: 0.8842 (tp30) REVERT: C 90 ASP cc_start: 0.8898 (t0) cc_final: 0.8606 (t70) REVERT: D 27 ARG cc_start: 0.6677 (tmt170) cc_final: 0.6236 (tmt170) REVERT: D 32 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7798 (mm-30) REVERT: D 90 GLU cc_start: 0.8532 (mp0) cc_final: 0.8296 (mp0) REVERT: E 50 GLU cc_start: 0.9173 (tt0) cc_final: 0.8874 (tt0) REVERT: E 54 TYR cc_start: 0.8914 (m-80) cc_final: 0.8581 (m-10) REVERT: F 44 LYS cc_start: 0.9404 (tptm) cc_final: 0.9154 (tppp) REVERT: F 84 MET cc_start: 0.8879 (mmm) cc_final: 0.7960 (tpp) REVERT: G 61 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8709 (tm-30) REVERT: G 64 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8880 (tm-30) REVERT: G 90 ASP cc_start: 0.8442 (t0) cc_final: 0.8010 (t0) REVERT: G 93 LEU cc_start: 0.9524 (mm) cc_final: 0.9244 (mt) REVERT: G 101 THR cc_start: 0.8958 (m) cc_final: 0.8486 (p) REVERT: N 167 TYR cc_start: 0.9123 (m-10) cc_final: 0.8771 (m-80) REVERT: N 276 LEU cc_start: 0.9268 (mp) cc_final: 0.8825 (mt) REVERT: K 3816 MET cc_start: 0.5402 (ttt) cc_final: 0.4804 (mtt) REVERT: T 315 MET cc_start: -0.0795 (mmp) cc_final: -0.1455 (mmt) REVERT: T 500 MET cc_start: 0.5494 (mtt) cc_final: 0.5063 (mtt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3805 time to fit residues: 100.8610 Evaluate side-chains 147 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 30.0000 chunk 114 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 181 optimal weight: 0.0000 chunk 157 optimal weight: 50.0000 chunk 16 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 chunk 96 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 overall best weight: 3.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN N 12 ASN ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20876 Z= 0.252 Angle : 0.588 9.598 29457 Z= 0.335 Chirality : 0.039 0.200 3307 Planarity : 0.004 0.047 2724 Dihedral : 27.716 170.830 5095 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.15 (0.20), residues: 1729 helix: 2.05 (0.22), residues: 551 sheet: -2.33 (0.32), residues: 243 loop : -2.19 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 95 HIS 0.006 0.001 HIS R 178 PHE 0.012 0.001 PHE G 25 TYR 0.020 0.001 TYR D 80 ARG 0.007 0.000 ARG D 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.9029 (t) cc_final: 0.8794 (t) REVERT: A 50 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8742 (mt-10) REVERT: A 90 MET cc_start: 0.9390 (mmt) cc_final: 0.8959 (mmm) REVERT: A 94 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8759 (mm-30) REVERT: A 97 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8313 (mt-10) REVERT: A 120 MET cc_start: 0.8958 (mtt) cc_final: 0.8442 (mtt) REVERT: B 25 ASN cc_start: 0.8549 (m110) cc_final: 0.8194 (m110) REVERT: B 63 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8686 (mt-10) REVERT: B 84 MET cc_start: 0.8863 (mmm) cc_final: 0.8413 (mmm) REVERT: C 56 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8241 (mm-30) REVERT: C 61 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8688 (tm-30) REVERT: C 64 GLU cc_start: 0.9162 (tp30) cc_final: 0.8819 (tp30) REVERT: C 90 ASP cc_start: 0.8848 (t0) cc_final: 0.8534 (t70) REVERT: D 27 ARG cc_start: 0.6750 (tmt170) cc_final: 0.6288 (tmt170) REVERT: D 32 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7641 (mm-30) REVERT: D 90 GLU cc_start: 0.8582 (mp0) cc_final: 0.8323 (mp0) REVERT: E 50 GLU cc_start: 0.9173 (tt0) cc_final: 0.8898 (tt0) REVERT: E 54 TYR cc_start: 0.8874 (m-80) cc_final: 0.8508 (m-10) REVERT: F 44 LYS cc_start: 0.9405 (tptm) cc_final: 0.9137 (tppp) REVERT: F 79 LYS cc_start: 0.9531 (mttm) cc_final: 0.9111 (mtmt) REVERT: F 84 MET cc_start: 0.8736 (mmm) cc_final: 0.8124 (tpp) REVERT: G 61 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8660 (tm-30) REVERT: G 64 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8873 (tm-30) REVERT: G 75 LYS cc_start: 0.9524 (mmtt) cc_final: 0.9030 (tptt) REVERT: G 90 ASP cc_start: 0.8369 (t0) cc_final: 0.7981 (t70) REVERT: G 93 LEU cc_start: 0.9521 (mm) cc_final: 0.9303 (mt) REVERT: G 101 THR cc_start: 0.8928 (m) cc_final: 0.8468 (p) REVERT: H 56 MET cc_start: 0.9273 (tpt) cc_final: 0.9058 (tpp) REVERT: N 167 TYR cc_start: 0.9123 (m-10) cc_final: 0.8768 (m-80) REVERT: N 276 LEU cc_start: 0.9230 (mp) cc_final: 0.8804 (mt) REVERT: K 3816 MET cc_start: 0.5323 (ttt) cc_final: 0.4733 (mtt) REVERT: R 241 TRP cc_start: 0.8249 (m100) cc_final: 0.7887 (m100) REVERT: T 315 MET cc_start: -0.0837 (mmp) cc_final: -0.1170 (tpt) REVERT: T 500 MET cc_start: 0.5357 (mtt) cc_final: 0.4865 (mtt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.3717 time to fit residues: 104.0563 Evaluate side-chains 156 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 144 optimal weight: 30.0000 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 157 optimal weight: 40.0000 chunk 65 optimal weight: 0.8980 chunk 161 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN N 12 ASN N 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.063074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.033678 restraints weight = 142590.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.034898 restraints weight = 69916.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.035623 restraints weight = 44130.342| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20876 Z= 0.183 Angle : 0.560 12.572 29457 Z= 0.319 Chirality : 0.038 0.204 3307 Planarity : 0.004 0.046 2724 Dihedral : 27.575 173.937 5095 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.93 (0.21), residues: 1729 helix: 2.34 (0.22), residues: 552 sheet: -2.25 (0.32), residues: 231 loop : -2.13 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 95 HIS 0.012 0.001 HIS R 178 PHE 0.024 0.001 PHE E 104 TYR 0.016 0.001 TYR D 80 ARG 0.007 0.000 ARG D 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.01 seconds wall clock time: 67 minutes 26.40 seconds (4046.40 seconds total)