Starting phenix.real_space_refine (version: dev) on Fri Dec 16 01:18:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiz_0695/12_2022/6kiz_0695_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiz_0695/12_2022/6kiz_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_0695/12_2022/6kiz_0695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiz_0695/12_2022/6kiz_0695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiz_0695/12_2022/6kiz_0695_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiz_0695/12_2022/6kiz_0695_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 11.78, per 1000 atoms: 0.59 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: 10.15 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: 7.35 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: 8.03 Time building geometry restraints manager: 10.69 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: 10027 34.36 - 68.71: 1428 68.71 - 103.07: 39 103.07 - 137.42: 1 137.42 - 171.78: 3 Dihedral angle restraints: 11498 sinusoidal: 6394 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 11495 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 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. 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: 0.010 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 6.150 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.180 Process input model: 63.200 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 : 23.167 171.777 8208 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 1.922 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 outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.4426 time to fit residues: 195.8747 Evaluate side-chains 173 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.915 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4123 ------------------------------------------------------------------------------- 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: 6.9990 chunk 83 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 20876 Z= 0.297 Angle : 0.627 7.070 29457 Z= 0.361 Chirality : 0.041 0.189 3307 Planarity : 0.004 0.041 2724 Dihedral : 28.541 169.755 4843 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.00 % 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: -1.89 (0.19), residues: 1729 helix: 1.47 (0.22), residues: 548 sheet: -2.69 (0.31), residues: 228 loop : -2.70 (0.17), residues: 953 *********************** 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 215 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.860 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 outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.3588 time to fit residues: 113.3859 Evaluate side-chains 165 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4342 ------------------------------------------------------------------------------- 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: 0.0070 chunk 55 optimal weight: 5.9990 chunk 149 optimal weight: 30.0000 chunk 122 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 194 optimal weight: 50.0000 chunk 160 optimal weight: 8.9990 chunk 178 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 overall best weight: 5.2006 ------------------------------------------------------------------------------- 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: 0.8328 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 20876 Z= 0.349 Angle : 0.636 7.774 29457 Z= 0.363 Chirality : 0.041 0.152 3307 Planarity : 0.004 0.044 2724 Dihedral : 28.376 166.482 4843 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer Outliers : 0.07 % 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: -1.60 (0.20), residues: 1729 helix: 1.75 (0.22), residues: 548 sheet: -2.52 (0.31), residues: 225 loop : -2.54 (0.18), residues: 956 *********************** 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 206 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.3651 time to fit residues: 110.1060 Evaluate side-chains 147 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4308 ------------------------------------------------------------------------------- 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: 8.9990 chunk 135 optimal weight: 30.0000 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 180 optimal weight: 30.0000 chunk 191 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 171 optimal weight: 40.0000 chunk 51 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 E 68 GLN F 25 ASN N 12 ASN ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K3906 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3114 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= 0.340 Angle : 0.620 8.151 29457 Z= 0.355 Chirality : 0.040 0.150 3307 Planarity : 0.004 0.039 2724 Dihedral : 28.285 166.966 4843 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer Outliers : 0.00 % 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: -1.53 (0.20), residues: 1729 helix: 1.83 (0.22), residues: 549 sheet: -2.61 (0.30), residues: 238 loop : -2.47 (0.18), residues: 942 *********************** 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 191 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.917 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 outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.3488 time to fit residues: 98.6546 Evaluate side-chains 146 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1964 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 40.0000 chunk 78 optimal weight: 7.9990 chunk 163 optimal weight: 0.3980 chunk 132 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 171 optimal weight: 50.0000 chunk 48 optimal weight: 0.8980 overall best weight: 3.4586 ------------------------------------------------------------------------------- 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** ** K3861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3906 ASN R 86 HIS ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3334 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 : 0.573 7.449 29457 Z= 0.330 Chirality : 0.039 0.165 3307 Planarity : 0.004 0.041 2724 Dihedral : 28.162 169.974 4843 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 0.00 % 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: -1.34 (0.20), residues: 1729 helix: 2.09 (0.22), residues: 549 sheet: -2.58 (0.31), residues: 241 loop : -2.40 (0.19), residues: 939 *********************** 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 194 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.977 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 outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3931 time to fit residues: 113.1457 Evaluate side-chains 153 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.888 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4232 ------------------------------------------------------------------------------- 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: 0.0970 chunk 172 optimal weight: 0.0070 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 50.0000 chunk 47 optimal weight: 4.9990 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: 1.8202 ------------------------------------------------------------------------------- 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** ** K3861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 20876 Z= 0.176 Angle : 0.539 7.633 29457 Z= 0.311 Chirality : 0.038 0.143 3307 Planarity : 0.004 0.043 2724 Dihedral : 28.018 172.868 4843 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.00 % 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: -1.08 (0.21), residues: 1729 helix: 2.47 (0.22), residues: 548 sheet: -2.43 (0.32), residues: 229 loop : -2.36 (0.18), residues: 952 *********************** 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 205 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.039 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 outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.3425 time to fit residues: 104.6241 Evaluate side-chains 159 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.040 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5868 ------------------------------------------------------------------------------- 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: 0.0980 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 139 optimal weight: 30.0000 chunk 108 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 190 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 116 optimal weight: 0.4980 chunk 88 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3907 HIS ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3782 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= 0.174 Angle : 0.536 7.598 29457 Z= 0.310 Chirality : 0.038 0.145 3307 Planarity : 0.003 0.044 2724 Dihedral : 27.944 172.882 4843 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.00 % 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: -1.10 (0.21), residues: 1729 helix: 2.32 (0.22), residues: 558 sheet: -2.45 (0.31), residues: 247 loop : -2.30 (0.19), residues: 924 *********************** 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 201 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.888 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 outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.3381 time to fit residues: 101.9714 Evaluate side-chains 155 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.952 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4255 ------------------------------------------------------------------------------- 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: 9.9990 chunk 76 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 150 optimal weight: 0.0030 overall best weight: 3.3998 ------------------------------------------------------------------------------- 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** ** K3861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3884 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 : 0.564 9.568 29457 Z= 0.324 Chirality : 0.038 0.142 3307 Planarity : 0.004 0.044 2724 Dihedral : 27.938 170.696 4843 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.00 % 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: -1.12 (0.20), residues: 1729 helix: 2.19 (0.22), residues: 557 sheet: -2.31 (0.31), residues: 247 loop : -2.28 (0.19), residues: 925 *********************** 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 186 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.078 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 outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.3580 time to fit residues: 99.0690 Evaluate side-chains 150 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4639 ------------------------------------------------------------------------------- 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: 50.0000 chunk 182 optimal weight: 5.9990 chunk 166 optimal weight: 50.0000 chunk 177 optimal weight: 4.9990 chunk 107 optimal weight: 0.0670 chunk 77 optimal weight: 8.9990 chunk 139 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 160 optimal weight: 40.0000 chunk 168 optimal weight: 5.9990 chunk 116 optimal weight: 30.0000 overall best weight: 5.2126 ------------------------------------------------------------------------------- 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** ** K3861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 20876 Z= 0.342 Angle : 0.628 11.814 29457 Z= 0.353 Chirality : 0.040 0.143 3307 Planarity : 0.004 0.047 2724 Dihedral : 28.004 168.289 4843 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 0.00 % 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: -1.18 (0.20), residues: 1729 helix: 2.06 (0.22), residues: 545 sheet: -2.22 (0.32), residues: 250 loop : -2.24 (0.19), residues: 934 *********************** 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 183 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 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 outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3515 time to fit residues: 96.1113 Evaluate side-chains 149 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.927 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4176 ------------------------------------------------------------------------------- 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: 40.0000 chunk 114 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 181 optimal weight: 0.0980 chunk 157 optimal weight: 30.0000 chunk 16 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 overall best weight: 4.6188 ------------------------------------------------------------------------------- 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** ** K3861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 20876 Z= 0.309 Angle : 0.612 10.492 29457 Z= 0.347 Chirality : 0.040 0.212 3307 Planarity : 0.004 0.049 2724 Dihedral : 28.010 169.154 4843 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 0.00 % 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: -1.16 (0.20), residues: 1729 helix: 1.96 (0.22), residues: 551 sheet: -2.12 (0.32), residues: 255 loop : -2.19 (0.19), residues: 923 ********************** 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 181 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.011 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 outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3595 time to fit residues: 97.4180 Evaluate side-chains 147 residues out of total 1504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5804 ------------------------------------------------------------------------------- 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: 9.9990 chunk 48 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 157 optimal weight: 50.0000 chunk 65 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- 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** ** K3861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.062129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.032995 restraints weight = 144313.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.034111 restraints weight = 71153.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.034833 restraints weight = 45251.241| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 20876 Z= 0.250 Angle : 0.578 10.216 29457 Z= 0.331 Chirality : 0.039 0.197 3307 Planarity : 0.004 0.048 2724 Dihedral : 27.957 170.738 4843 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 0.00 % 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: -1.03 (0.21), residues: 1729 helix: 2.08 (0.22), residues: 551 sheet: -2.03 (0.32), residues: 256 loop : -2.13 (0.19), residues: 922 =============================================================================== Job complete usr+sys time: 3346.20 seconds wall clock time: 62 minutes 22.09 seconds (3742.09 seconds total)