Starting phenix.real_space_refine on Thu Mar 21 04:46:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/03_2024/6kiv_9999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/03_2024/6kiv_9999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/03_2024/6kiv_9999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/03_2024/6kiv_9999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/03_2024/6kiv_9999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiv_9999/03_2024/6kiv_9999_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8596 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 290 5.49 5 S 61 5.16 5 C 12166 2.51 5 N 3759 2.21 5 O 4442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 3916": "NH1" <-> "NH2" Residue "K ARG 3936": "NH1" <-> "NH2" Residue "K ARG 3965": "NH1" <-> "NH2" Residue "N ARG 76": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N ARG 190": "NH1" <-> "NH2" Residue "N ARG 228": "NH1" <-> "NH2" Residue "N ARG 272": "NH1" <-> "NH2" Residue "T TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20719 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "D" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1434 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2881 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 14, 'TRANS': 351} Chain breaks: 1 Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "T" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1399 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 12, 'TRANS': 163} Chain breaks: 1 Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2326 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13389 SG CYS K3957 39.155 70.820 42.538 1.00167.86 S ATOM 13403 SG CYS K3959 42.422 71.072 44.036 1.00163.71 S Time building chain proxies: 10.85, per 1000 atoms: 0.52 Number of scatterers: 20719 At special positions: 0 Unit cell: (151.51, 141.7, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 61 16.00 P 290 15.00 O 4442 8.00 N 3759 7.00 C 12166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.50 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3957 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 23 sheets defined 27.6% alpha, 10.1% beta 145 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 9.04 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 87 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 33 through 41 Processing helix chain 'B' and resid 50 through 75 removed outlier: 4.858A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.917A 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 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 119 removed outlier: 4.201A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 87 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 50 through 75 removed outlier: 4.461A 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: 3.664A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'K' and resid 3816 through 3830 removed outlier: 5.517A pdb=" N LYS K3828 " --> pdb=" O LYS K3824 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU K3829 " --> pdb=" O LYS K3825 " (cutoff:3.500A) Processing helix chain 'K' and resid 3867 through 3877 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'O' and resid 23 through 33 Processing helix chain 'O' and resid 38 through 40 No H-bonds generated for 'chain 'O' and resid 38 through 40' Processing helix chain 'O' and resid 56 through 58 No H-bonds generated for 'chain 'O' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'K' and resid 3831 through 3835 removed outlier: 4.089A pdb=" N GLY K3832 " --> pdb=" O PHE K3844 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 3884 through 3886 Processing sheet with id= C, first strand: chain 'K' and resid 3915 through 3920 removed outlier: 3.951A pdb=" N ARG K3916 " --> pdb=" O VAL K3927 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL K3927 " --> pdb=" O ARG K3916 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE K3918 " --> pdb=" O HIS K3925 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS K3925 " --> pdb=" O ILE K3918 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE K3920 " --> pdb=" O GLN K3923 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN K3923 " --> pdb=" O ILE K3920 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'N' and resid 30 through 32 removed outlier: 3.586A pdb=" N THR N 31 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'N' and resid 80 through 83 removed outlier: 4.002A pdb=" N SER N 83 " --> pdb=" O SER N 91 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'N' and resid 112 through 115 removed outlier: 4.168A pdb=" N LYS N 112 " --> pdb=" O CYS N 126 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN N 114 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL N 123 " --> pdb=" O LEU N 135 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'N' and resid 156 through 159 Processing sheet with id= H, first strand: chain 'N' and resid 174 through 177 removed outlier: 3.940A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 243 through 245 removed outlier: 3.877A pdb=" N GLU N 205 " --> pdb=" O LEU N 214 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER N 203 " --> pdb=" O ASN N 216 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 254 through 259 removed outlier: 6.977A pdb=" N GLY N 269 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N CYS N 257 " --> pdb=" O VAL N 267 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL N 267 " --> pdb=" O CYS N 257 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE N 259 " --> pdb=" O TYR N 265 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR N 265 " --> pdb=" O PHE N 259 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU N 280 " --> pdb=" O LEU N 286 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU N 286 " --> pdb=" O GLU N 280 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'O' and resid 2 through 6 Processing sheet with id= L, first strand: chain 'O' and resid 43 through 45 removed outlier: 4.114A pdb=" N LEU O 43 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 306 through 308 removed outlier: 3.722A pdb=" N VAL T 480 " --> pdb=" O VAL T 307 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'T' and resid 314 through 316 removed outlier: 3.545A pdb=" N VAL T 316 " --> pdb=" O ILE T 472 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'T' and resid 325 through 327 removed outlier: 3.647A pdb=" N GLY T 325 " --> pdb=" O LEU T 398 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU T 398 " --> pdb=" O GLY T 325 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP T 327 " --> pdb=" O ILE T 396 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE T 396 " --> pdb=" O TRP T 327 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'T' and resid 372 through 374 removed outlier: 3.581A pdb=" N LYS T 380 " --> pdb=" O LYS T 373 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'R' and resid 68 through 72 removed outlier: 3.929A pdb=" N LEU R 68 " --> pdb=" O SER R 64 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS R 70 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA R 61 " --> pdb=" O LYS R 52 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS R 52 " --> pdb=" O ALA R 61 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 101 through 104 removed outlier: 3.577A pdb=" N LYS R 112 " --> pdb=" O SER R 104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'R' and resid 177 through 179 removed outlier: 5.738A pdb=" N ASP R 199 " --> pdb=" O CYS R 205 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N CYS R 205 " --> pdb=" O ASP R 199 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'R' and resid 219 through 222 removed outlier: 3.615A pdb=" N LYS R 239 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'R' and resid 264 through 266 Processing sheet with id= V, first strand: chain 'R' and resid 153 through 156 Processing sheet with id= W, first strand: chain 'R' and resid 304 through 309 removed outlier: 7.428A pdb=" N ALA R 319 " --> pdb=" O ILE R 305 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR R 307 " --> pdb=" O ALA R 317 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA R 317 " --> pdb=" O THR R 307 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 8.28 Time building geometry restraints manager: 10.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4052 1.33 - 1.45: 6267 1.45 - 1.57: 10731 1.57 - 1.69: 578 1.69 - 1.81: 88 Bond restraints: 21716 Sorted by residual: bond pdb=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.375 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" C2 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.330 1.378 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C6 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.338 1.386 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.491 -0.069 3.00e-02 1.11e+03 5.28e+00 ... (remaining 21711 not shown) Histogram of bond angle deviations from ideal: 89.61 - 98.52: 10 98.52 - 107.43: 2740 107.43 - 116.34: 13589 116.34 - 125.25: 13075 125.25 - 134.15: 1171 Bond angle restraints: 30585 Sorted by residual: angle pdb=" CG SAH K4001 " pdb=" SD SAH K4001 " pdb=" C5' SAH K4001 " ideal model delta sigma weight residual 101.77 89.61 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 122.48 -9.30 2.37e+00 1.78e-01 1.54e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 125.89 -5.69 1.50e+00 4.44e-01 1.44e+01 angle pdb=" CA ARG G 99 " pdb=" CB ARG G 99 " pdb=" CG ARG G 99 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N GLN N 323 " pdb=" CA GLN N 323 " pdb=" C GLN N 323 " ideal model delta sigma weight residual 110.80 118.14 -7.34 2.13e+00 2.20e-01 1.19e+01 ... (remaining 30580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 10875 35.82 - 71.65: 1373 71.65 - 107.47: 25 107.47 - 143.29: 4 143.29 - 179.11: 1 Dihedral angle restraints: 12278 sinusoidal: 6877 harmonic: 5401 Sorted by residual: dihedral pdb=" CA LYS B 31 " pdb=" C LYS B 31 " pdb=" N PRO B 32 " pdb=" CA PRO B 32 " ideal model delta harmonic sigma weight residual 180.00 133.83 46.17 0 5.00e+00 4.00e-02 8.53e+01 dihedral pdb=" CA ASN K3779 " pdb=" C ASN K3779 " pdb=" N PHE K3780 " pdb=" CA PHE K3780 " ideal model delta harmonic sigma weight residual 180.00 138.88 41.12 0 5.00e+00 4.00e-02 6.76e+01 dihedral pdb=" CA TYR N 13 " pdb=" C TYR N 13 " pdb=" N PRO N 14 " pdb=" CA PRO N 14 " ideal model delta harmonic sigma weight residual -180.00 -143.60 -36.40 0 5.00e+00 4.00e-02 5.30e+01 ... (remaining 12275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2253 0.046 - 0.092: 872 0.092 - 0.138: 258 0.138 - 0.184: 49 0.184 - 0.230: 6 Chirality restraints: 3438 Sorted by residual: chirality pdb=" C1' SAH K4001 " pdb=" C2' SAH K4001 " pdb=" N9 SAH K4001 " pdb=" O4' SAH K4001 " both_signs ideal model delta sigma weight residual False 2.35 2.58 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3435 not shown) Planarity restraints: 2870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO B 32 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN K3779 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" CG ASN K3779 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN K3779 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN K3779 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K3768 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C VAL K3768 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL K3768 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS K3769 " -0.015 2.00e-02 2.50e+03 ... (remaining 2867 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4499 2.79 - 3.32: 17455 3.32 - 3.85: 37486 3.85 - 4.37: 41580 4.37 - 4.90: 64188 Nonbonded interactions: 165208 Sorted by model distance: nonbonded pdb=" OG SER R 129 " pdb=" OD2 ASP R 150 " model vdw 2.263 2.440 nonbonded pdb=" OG SER R 96 " pdb=" OD1 ASP R 98 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.265 2.440 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.265 2.440 nonbonded pdb=" OG SER R 49 " pdb=" O SER R 63 " model vdw 2.268 2.440 ... (remaining 165203 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 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = (chain 'H' and resid 28 through 120) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 5.370 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 63.920 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 21716 Z= 0.424 Angle : 0.904 12.590 30585 Z= 0.511 Chirality : 0.053 0.230 3438 Planarity : 0.007 0.108 2870 Dihedral : 22.703 179.114 8794 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.16), residues: 1830 helix: -1.38 (0.17), residues: 568 sheet: -2.89 (0.26), residues: 312 loop : -3.18 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP N 303 HIS 0.010 0.002 HIS B 75 PHE 0.023 0.003 PHE N 189 TYR 0.031 0.003 TYR B 51 ARG 0.009 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9254 (p) cc_final: 0.8948 (p) REVERT: A 123 ASP cc_start: 0.8318 (m-30) cc_final: 0.8094 (m-30) REVERT: B 35 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8090 (ttm-80) REVERT: B 58 LEU cc_start: 0.8871 (tp) cc_final: 0.8573 (tt) REVERT: B 92 ARG cc_start: 0.8717 (mtp-110) cc_final: 0.8398 (mtp-110) REVERT: D 27 ARG cc_start: 0.7875 (tmt170) cc_final: 0.7629 (tmt-80) REVERT: D 54 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8811 (mmmm) REVERT: D 65 ASP cc_start: 0.8143 (t0) cc_final: 0.7866 (t0) REVERT: D 81 ASN cc_start: 0.8438 (m-40) cc_final: 0.8148 (m110) REVERT: D 88 SER cc_start: 0.9070 (p) cc_final: 0.8866 (p) REVERT: F 88 TYR cc_start: 0.8891 (m-10) cc_final: 0.7805 (m-10) REVERT: G 18 SER cc_start: 0.8315 (m) cc_final: 0.7614 (p) REVERT: G 42 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7727 (mtm-85) REVERT: G 61 GLU cc_start: 0.8672 (tp30) cc_final: 0.8331 (tm-30) REVERT: H 73 GLU cc_start: 0.8267 (tp30) cc_final: 0.8037 (mt-10) REVERT: H 80 TYR cc_start: 0.7333 (m-10) cc_final: 0.6582 (m-10) REVERT: H 82 LYS cc_start: 0.8942 (mttt) cc_final: 0.8089 (mmtt) REVERT: K 3828 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8215 (pttt) REVERT: K 3846 LYS cc_start: 0.6392 (mtmt) cc_final: 0.6074 (tmtt) REVERT: N 60 LYS cc_start: 0.8170 (tptt) cc_final: 0.7547 (tppt) REVERT: N 115 TYR cc_start: 0.5656 (m-80) cc_final: 0.5121 (m-10) REVERT: N 226 ASP cc_start: 0.7903 (t0) cc_final: 0.7649 (t0) REVERT: N 320 ILE cc_start: 0.8932 (mp) cc_final: 0.8636 (pt) REVERT: T 503 MET cc_start: 0.6152 (mmm) cc_final: 0.5486 (mtm) REVERT: R 72 TRP cc_start: 0.6754 (m100) cc_final: 0.5447 (m100) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.4368 time to fit residues: 311.0209 Evaluate side-chains 290 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 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 31 HIS C 38 ASN C 84 GLN C 94 ASN G 89 ASN G 110 ASN N 79 HIS N 273 GLN N 328 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 381 HIS ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21716 Z= 0.211 Angle : 0.636 8.918 30585 Z= 0.361 Chirality : 0.041 0.165 3438 Planarity : 0.005 0.088 2870 Dihedral : 27.525 177.829 5203 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.45 % Allowed : 11.54 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.18), residues: 1830 helix: 0.55 (0.21), residues: 564 sheet: -2.58 (0.27), residues: 287 loop : -2.93 (0.17), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 198 HIS 0.012 0.001 HIS R 44 PHE 0.018 0.002 PHE N 189 TYR 0.034 0.002 TYR B 51 ARG 0.006 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 340 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8570 (m-30) cc_final: 0.8266 (m-30) REVERT: B 88 TYR cc_start: 0.8678 (m-10) cc_final: 0.7295 (m-80) REVERT: B 92 ARG cc_start: 0.8578 (mtp-110) cc_final: 0.8336 (ttp80) REVERT: D 44 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8310 (tm-30) REVERT: D 54 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8828 (mmmm) REVERT: D 88 SER cc_start: 0.8971 (p) cc_final: 0.8701 (p) REVERT: E 73 GLU cc_start: 0.8146 (tt0) cc_final: 0.7902 (tt0) REVERT: F 64 ASN cc_start: 0.8945 (t0) cc_final: 0.8635 (t0) REVERT: F 88 TYR cc_start: 0.8763 (m-10) cc_final: 0.8448 (m-10) REVERT: G 18 SER cc_start: 0.8319 (m) cc_final: 0.7801 (p) REVERT: G 55 LEU cc_start: 0.9020 (mt) cc_final: 0.8820 (mt) REVERT: H 82 LYS cc_start: 0.8574 (mttt) cc_final: 0.7918 (mmtt) REVERT: K 3846 LYS cc_start: 0.6636 (mtmt) cc_final: 0.6061 (tmtt) REVERT: K 3857 GLU cc_start: 0.7693 (tt0) cc_final: 0.7460 (tp30) REVERT: K 3867 GLN cc_start: 0.7573 (mp10) cc_final: 0.7370 (mp10) REVERT: K 3873 LYS cc_start: 0.8057 (ptmt) cc_final: 0.7705 (ptpp) REVERT: K 3876 ASP cc_start: 0.8367 (m-30) cc_final: 0.7461 (p0) REVERT: N 51 TRP cc_start: 0.4880 (t60) cc_final: 0.3727 (t60) REVERT: N 226 ASP cc_start: 0.8023 (t0) cc_final: 0.7244 (t0) REVERT: N 320 ILE cc_start: 0.8943 (mp) cc_final: 0.8626 (pt) REVERT: N 340 ASP cc_start: 0.8813 (t0) cc_final: 0.8545 (t0) REVERT: T 336 MET cc_start: 0.5188 (mmm) cc_final: 0.4860 (mmm) REVERT: T 503 MET cc_start: 0.6359 (mmm) cc_final: 0.5860 (mpp) REVERT: R 72 TRP cc_start: 0.6362 (m100) cc_final: 0.5772 (m100) REVERT: R 284 TYR cc_start: 0.1008 (m-10) cc_final: 0.0715 (m-80) outliers start: 55 outliers final: 37 residues processed: 375 average time/residue: 0.3435 time to fit residues: 191.1577 Evaluate side-chains 306 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 269 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 3848 ASN Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 315 SER Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 52 optimal weight: 0.0870 chunk 189 optimal weight: 8.9990 chunk 204 optimal weight: 40.0000 chunk 168 optimal weight: 8.9990 chunk 187 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN N 250 ASN N 273 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21716 Z= 0.193 Angle : 0.596 9.825 30585 Z= 0.338 Chirality : 0.040 0.187 3438 Planarity : 0.004 0.079 2870 Dihedral : 27.363 177.721 5203 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.76 % Allowed : 13.35 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.19), residues: 1830 helix: 1.43 (0.22), residues: 553 sheet: -2.42 (0.26), residues: 312 loop : -2.75 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 59 HIS 0.008 0.001 HIS R 44 PHE 0.022 0.001 PHE N 189 TYR 0.023 0.002 TYR N 115 ARG 0.005 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 307 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8974 (p) cc_final: 0.8672 (p) REVERT: A 120 MET cc_start: 0.7493 (mmt) cc_final: 0.7272 (mmm) REVERT: A 123 ASP cc_start: 0.8435 (m-30) cc_final: 0.8186 (m-30) REVERT: B 84 MET cc_start: 0.7584 (mmt) cc_final: 0.6084 (mmm) REVERT: B 88 TYR cc_start: 0.7299 (m-10) cc_final: 0.7005 (m-10) REVERT: B 92 ARG cc_start: 0.8574 (mtp-110) cc_final: 0.8319 (ttp80) REVERT: D 48 ASP cc_start: 0.6845 (t0) cc_final: 0.6532 (t0) REVERT: D 54 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8819 (mmmm) REVERT: D 88 SER cc_start: 0.8987 (p) cc_final: 0.8780 (p) REVERT: E 73 GLU cc_start: 0.8048 (tt0) cc_final: 0.7829 (tt0) REVERT: F 84 MET cc_start: 0.7319 (tpp) cc_final: 0.6938 (tpp) REVERT: F 88 TYR cc_start: 0.8617 (m-10) cc_final: 0.7538 (m-10) REVERT: G 55 LEU cc_start: 0.9024 (mt) cc_final: 0.8793 (mt) REVERT: H 80 TYR cc_start: 0.7482 (m-10) cc_final: 0.7013 (m-80) REVERT: H 82 LYS cc_start: 0.8374 (mttt) cc_final: 0.7830 (mmtt) REVERT: K 3873 LYS cc_start: 0.8104 (ptmt) cc_final: 0.7882 (ptpp) REVERT: K 3876 ASP cc_start: 0.8466 (m-30) cc_final: 0.7560 (p0) REVERT: N 226 ASP cc_start: 0.7983 (t0) cc_final: 0.7070 (t0) REVERT: N 300 ASP cc_start: 0.7610 (m-30) cc_final: 0.7315 (m-30) REVERT: N 320 ILE cc_start: 0.8918 (mp) cc_final: 0.8624 (pt) REVERT: T 500 MET cc_start: 0.0035 (ptm) cc_final: -0.0644 (ptm) REVERT: T 503 MET cc_start: 0.6346 (mmm) cc_final: 0.5549 (mpp) REVERT: R 72 TRP cc_start: 0.6384 (m100) cc_final: 0.5657 (m100) REVERT: R 140 GLN cc_start: 0.4413 (mt0) cc_final: 0.3696 (mm110) outliers start: 60 outliers final: 46 residues processed: 343 average time/residue: 0.3279 time to fit residues: 172.0539 Evaluate side-chains 310 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 264 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3848 ASN Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3919 ASN Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 233 CYS Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 315 SER Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 384 SER Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 286 TRP Chi-restraints excluded: chain R residue 301 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 20 optimal weight: 0.0570 chunk 90 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 201 optimal weight: 40.0000 chunk 99 optimal weight: 10.0000 chunk 179 optimal weight: 40.0000 chunk 54 optimal weight: 0.7980 overall best weight: 2.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN H 64 ASN N 12 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21716 Z= 0.261 Angle : 0.625 11.907 30585 Z= 0.351 Chirality : 0.041 0.188 3438 Planarity : 0.004 0.077 2870 Dihedral : 27.425 177.715 5203 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.83 % Allowed : 14.23 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.19), residues: 1830 helix: 1.36 (0.22), residues: 548 sheet: -2.31 (0.28), residues: 300 loop : -2.64 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 156 HIS 0.006 0.001 HIS F 75 PHE 0.017 0.001 PHE K3885 TYR 0.024 0.002 TYR H 37 ARG 0.004 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 272 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9096 (p) cc_final: 0.8871 (p) REVERT: A 123 ASP cc_start: 0.8436 (m-30) cc_final: 0.8186 (m-30) REVERT: B 31 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7926 (tptt) REVERT: B 84 MET cc_start: 0.7879 (mmt) cc_final: 0.7677 (mmm) REVERT: D 44 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8437 (tm-30) REVERT: D 48 ASP cc_start: 0.6891 (t0) cc_final: 0.6523 (t0) REVERT: D 54 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8879 (mmmm) REVERT: E 73 GLU cc_start: 0.8049 (tt0) cc_final: 0.7829 (tt0) REVERT: E 133 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7397 (tt0) REVERT: F 84 MET cc_start: 0.7343 (tpp) cc_final: 0.6955 (tpp) REVERT: F 88 TYR cc_start: 0.8649 (m-10) cc_final: 0.7460 (m-10) REVERT: F 92 ARG cc_start: 0.8966 (mtp-110) cc_final: 0.8331 (ttp80) REVERT: G 55 LEU cc_start: 0.9098 (mt) cc_final: 0.8873 (mt) REVERT: H 30 ARG cc_start: 0.8524 (mpt180) cc_final: 0.8090 (mmp80) REVERT: H 40 LYS cc_start: 0.9050 (mptt) cc_final: 0.8829 (mptt) REVERT: H 80 TYR cc_start: 0.7620 (m-10) cc_final: 0.7244 (m-80) REVERT: H 82 LYS cc_start: 0.8491 (mttt) cc_final: 0.7894 (mmtt) REVERT: K 3876 ASP cc_start: 0.8410 (m-30) cc_final: 0.7464 (p0) REVERT: K 3923 GLN cc_start: 0.8491 (pm20) cc_final: 0.8210 (pm20) REVERT: N 226 ASP cc_start: 0.7845 (t0) cc_final: 0.7347 (t0) REVERT: N 300 ASP cc_start: 0.7572 (m-30) cc_final: 0.7371 (m-30) REVERT: N 320 ILE cc_start: 0.9016 (mp) cc_final: 0.8766 (pt) REVERT: T 500 MET cc_start: -0.0071 (ptm) cc_final: -0.0948 (ptm) REVERT: T 503 MET cc_start: 0.6357 (mmm) cc_final: 0.5543 (mpp) REVERT: R 72 TRP cc_start: 0.6354 (m100) cc_final: 0.5516 (m100) REVERT: R 140 GLN cc_start: 0.4531 (mt0) cc_final: 0.3795 (mm110) outliers start: 77 outliers final: 62 residues processed: 320 average time/residue: 0.3191 time to fit residues: 156.1531 Evaluate side-chains 322 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 259 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3848 ASN Chi-restraints excluded: chain K residue 3867 GLN Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3919 ASN Chi-restraints excluded: chain K residue 3927 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 212 ASP Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 301 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 0.0570 chunk 114 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 82 optimal weight: 8.9990 chunk 171 optimal weight: 30.0000 chunk 138 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 375 HIS R 255 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21716 Z= 0.155 Angle : 0.561 9.786 30585 Z= 0.318 Chirality : 0.039 0.186 3438 Planarity : 0.003 0.072 2870 Dihedral : 27.181 176.164 5203 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.13 % Allowed : 16.80 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.19), residues: 1830 helix: 1.78 (0.22), residues: 559 sheet: -2.12 (0.28), residues: 314 loop : -2.58 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP T 346 HIS 0.005 0.001 HIS R 44 PHE 0.016 0.001 PHE N 189 TYR 0.022 0.001 TYR N 277 ARG 0.006 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 304 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9007 (p) cc_final: 0.8723 (p) REVERT: A 118 THR cc_start: 0.8444 (m) cc_final: 0.8112 (p) REVERT: A 120 MET cc_start: 0.7387 (mmt) cc_final: 0.7156 (mmm) REVERT: A 123 ASP cc_start: 0.8351 (m-30) cc_final: 0.8125 (m-30) REVERT: C 56 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7176 (tp30) REVERT: D 48 ASP cc_start: 0.6785 (t0) cc_final: 0.6419 (t0) REVERT: D 54 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8754 (mmmm) REVERT: E 73 GLU cc_start: 0.7986 (tt0) cc_final: 0.7767 (tt0) REVERT: E 133 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7281 (tt0) REVERT: F 92 ARG cc_start: 0.8831 (mtp-110) cc_final: 0.8278 (ttp80) REVERT: G 18 SER cc_start: 0.8371 (m) cc_final: 0.7956 (p) REVERT: G 55 LEU cc_start: 0.8989 (mt) cc_final: 0.8787 (mt) REVERT: G 92 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6793 (mm-30) REVERT: G 104 GLN cc_start: 0.8467 (mp10) cc_final: 0.7957 (mp10) REVERT: H 30 ARG cc_start: 0.8541 (mpt180) cc_final: 0.8035 (mmp80) REVERT: H 80 TYR cc_start: 0.7535 (m-10) cc_final: 0.7025 (m-80) REVERT: H 82 LYS cc_start: 0.8293 (mttt) cc_final: 0.7795 (mmtt) REVERT: K 3857 GLU cc_start: 0.6417 (tt0) cc_final: 0.6198 (tt0) REVERT: K 3876 ASP cc_start: 0.8424 (m-30) cc_final: 0.7455 (p0) REVERT: K 3925 HIS cc_start: 0.6257 (m-70) cc_final: 0.5750 (m90) REVERT: K 3940 LEU cc_start: 0.8590 (mm) cc_final: 0.8336 (mm) REVERT: N 134 MET cc_start: 0.7366 (ttp) cc_final: 0.7041 (tpp) REVERT: N 226 ASP cc_start: 0.7892 (t0) cc_final: 0.7436 (t0) REVERT: N 300 ASP cc_start: 0.7564 (m-30) cc_final: 0.7353 (m-30) REVERT: N 320 ILE cc_start: 0.8991 (mp) cc_final: 0.8743 (pt) REVERT: T 500 MET cc_start: -0.0150 (ptm) cc_final: -0.0919 (ptm) REVERT: T 503 MET cc_start: 0.6339 (mmm) cc_final: 0.5532 (mpp) REVERT: R 72 TRP cc_start: 0.6108 (m100) cc_final: 0.5251 (m100) REVERT: R 140 GLN cc_start: 0.5265 (mt0) cc_final: 0.4813 (mm110) REVERT: R 230 LEU cc_start: 0.6272 (tp) cc_final: 0.5677 (tp) outliers start: 50 outliers final: 35 residues processed: 330 average time/residue: 0.3284 time to fit residues: 164.3888 Evaluate side-chains 298 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 262 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain K residue 3816 MET Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3867 GLN Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3919 ASN Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 128 MET Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 372 ASP Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 222 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 39 optimal weight: 0.2980 chunk 118 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 201 optimal weight: 50.0000 chunk 167 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS K3906 ASN ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21716 Z= 0.244 Angle : 0.614 10.130 30585 Z= 0.344 Chirality : 0.041 0.202 3438 Planarity : 0.004 0.076 2870 Dihedral : 27.330 177.760 5203 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.45 % Allowed : 16.55 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.19), residues: 1830 helix: 1.52 (0.22), residues: 554 sheet: -1.96 (0.29), residues: 304 loop : -2.55 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 198 HIS 0.006 0.001 HIS F 75 PHE 0.015 0.001 PHE K3885 TYR 0.023 0.002 TYR H 37 ARG 0.004 0.000 ARG R 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 254 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9126 (p) cc_final: 0.8800 (p) REVERT: C 56 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: C 61 GLU cc_start: 0.8718 (tp30) cc_final: 0.8476 (tp30) REVERT: D 48 ASP cc_start: 0.6800 (t0) cc_final: 0.6385 (t0) REVERT: D 54 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8880 (mmmm) REVERT: E 133 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7352 (tt0) REVERT: F 84 MET cc_start: 0.7450 (tpp) cc_final: 0.7002 (tpp) REVERT: F 88 TYR cc_start: 0.8624 (m-10) cc_final: 0.7521 (m-10) REVERT: F 92 ARG cc_start: 0.8972 (mtp-110) cc_final: 0.8456 (ttp80) REVERT: G 104 GLN cc_start: 0.8658 (mp10) cc_final: 0.8137 (mp10) REVERT: H 80 TYR cc_start: 0.7646 (m-10) cc_final: 0.7302 (m-80) REVERT: H 82 LYS cc_start: 0.8336 (mttt) cc_final: 0.7792 (mmtt) REVERT: K 3828 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8167 (pttp) REVERT: K 3845 CYS cc_start: 0.8779 (OUTLIER) cc_final: 0.7976 (m) REVERT: K 3876 ASP cc_start: 0.8432 (m-30) cc_final: 0.7429 (p0) REVERT: K 3906 ASN cc_start: 0.6410 (m-40) cc_final: 0.6051 (m-40) REVERT: K 3923 GLN cc_start: 0.8276 (pm20) cc_final: 0.7989 (pm20) REVERT: K 3925 HIS cc_start: 0.6545 (m-70) cc_final: 0.6101 (m-70) REVERT: K 3943 ASP cc_start: 0.5918 (t0) cc_final: 0.5323 (t0) REVERT: N 133 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8399 (t) REVERT: N 134 MET cc_start: 0.7359 (ttp) cc_final: 0.7116 (tpp) REVERT: N 226 ASP cc_start: 0.7952 (t0) cc_final: 0.7530 (t0) REVERT: N 256 LYS cc_start: 0.8457 (tppt) cc_final: 0.8212 (tppt) REVERT: N 320 ILE cc_start: 0.9029 (mp) cc_final: 0.8798 (pt) REVERT: T 500 MET cc_start: -0.0093 (ptm) cc_final: -0.1029 (ptm) REVERT: T 503 MET cc_start: 0.6401 (mmm) cc_final: 0.5536 (mpp) REVERT: R 72 TRP cc_start: 0.6328 (m100) cc_final: 0.5369 (m100) REVERT: R 140 GLN cc_start: 0.5536 (mt0) cc_final: 0.4924 (mm110) REVERT: R 230 LEU cc_start: 0.6247 (tp) cc_final: 0.5586 (tp) outliers start: 71 outliers final: 56 residues processed: 297 average time/residue: 0.3044 time to fit residues: 139.9198 Evaluate side-chains 303 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 244 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3867 GLN Chi-restraints excluded: chain K residue 3868 THR Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3919 ASN Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 307 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 114 optimal weight: 0.0770 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 169 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 chunk 200 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** K3839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS R 295 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 21716 Z= 0.351 Angle : 0.692 9.826 30585 Z= 0.383 Chirality : 0.043 0.210 3438 Planarity : 0.004 0.080 2870 Dihedral : 27.531 177.493 5203 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.07 % Favored : 90.87 % Rotamer: Outliers : 5.64 % Allowed : 16.55 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.19), residues: 1830 helix: 0.98 (0.21), residues: 550 sheet: -2.09 (0.28), residues: 301 loop : -2.58 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 198 HIS 0.011 0.002 HIS K3839 PHE 0.020 0.002 PHE K3885 TYR 0.026 0.002 TYR N 13 ARG 0.005 0.001 ARG K3841 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 254 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9233 (p) cc_final: 0.8991 (p) REVERT: C 56 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7263 (tp30) REVERT: C 61 GLU cc_start: 0.8715 (tp30) cc_final: 0.8482 (tp30) REVERT: D 48 ASP cc_start: 0.7139 (t0) cc_final: 0.6716 (t0) REVERT: D 54 LYS cc_start: 0.9268 (mmmt) cc_final: 0.9038 (mmmt) REVERT: E 133 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7261 (tt0) REVERT: F 84 MET cc_start: 0.7538 (tpp) cc_final: 0.7112 (tpp) REVERT: F 88 TYR cc_start: 0.8675 (m-10) cc_final: 0.8160 (m-10) REVERT: F 92 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8262 (ttp80) REVERT: G 84 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: H 30 ARG cc_start: 0.8419 (mpt180) cc_final: 0.7849 (mmp80) REVERT: H 80 TYR cc_start: 0.7710 (m-10) cc_final: 0.7109 (m-10) REVERT: H 82 LYS cc_start: 0.8478 (mttt) cc_final: 0.7932 (mmtt) REVERT: K 3839 HIS cc_start: 0.7132 (p90) cc_final: 0.6889 (p-80) REVERT: K 3876 ASP cc_start: 0.8510 (m-30) cc_final: 0.7591 (p0) REVERT: N 226 ASP cc_start: 0.7728 (t0) cc_final: 0.7236 (t0) REVERT: N 320 ILE cc_start: 0.9131 (mp) cc_final: 0.8879 (pt) REVERT: T 500 MET cc_start: -0.0372 (ptm) cc_final: -0.1377 (ptm) REVERT: T 503 MET cc_start: 0.6104 (mmm) cc_final: 0.5698 (mpp) REVERT: R 72 TRP cc_start: 0.6420 (m100) cc_final: 0.5501 (m100) REVERT: R 140 GLN cc_start: 0.5738 (mt0) cc_final: 0.4914 (mm110) REVERT: R 230 LEU cc_start: 0.6147 (tp) cc_final: 0.5325 (tp) outliers start: 90 outliers final: 75 residues processed: 309 average time/residue: 0.3317 time to fit residues: 158.4608 Evaluate side-chains 319 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 241 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3843 LEU Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3848 ASN Chi-restraints excluded: chain K residue 3867 GLN Chi-restraints excluded: chain K residue 3868 THR Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3919 ASN Chi-restraints excluded: chain K residue 3926 ILE Chi-restraints excluded: chain K residue 3946 PHE Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain N residue 248 LEU Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 212 ASP Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 286 TRP Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 307 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 18 optimal weight: 0.3980 chunk 157 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21716 Z= 0.205 Angle : 0.605 9.506 30585 Z= 0.339 Chirality : 0.040 0.189 3438 Planarity : 0.004 0.076 2870 Dihedral : 27.295 175.637 5203 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.20 % Allowed : 18.68 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.19), residues: 1830 helix: 1.51 (0.22), residues: 549 sheet: -1.91 (0.29), residues: 286 loop : -2.54 (0.18), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 35 HIS 0.008 0.001 HIS R 170 PHE 0.013 0.001 PHE N 189 TYR 0.025 0.002 TYR N 115 ARG 0.004 0.000 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 264 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9172 (p) cc_final: 0.8869 (p) REVERT: B 84 MET cc_start: 0.7402 (tpt) cc_final: 0.6330 (tpt) REVERT: C 56 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7226 (tp30) REVERT: C 61 GLU cc_start: 0.8702 (tp30) cc_final: 0.8480 (tp30) REVERT: D 48 ASP cc_start: 0.6981 (t0) cc_final: 0.6561 (t0) REVERT: D 54 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8907 (mmmt) REVERT: F 84 MET cc_start: 0.7451 (tpp) cc_final: 0.7046 (tpp) REVERT: F 88 TYR cc_start: 0.8626 (m-10) cc_final: 0.8158 (m-10) REVERT: F 92 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8446 (ttp80) REVERT: G 24 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7926 (tp40) REVERT: G 55 LEU cc_start: 0.9052 (mt) cc_final: 0.8817 (mt) REVERT: G 84 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: H 30 ARG cc_start: 0.8488 (mpt180) cc_final: 0.7977 (mmp-170) REVERT: H 56 MET cc_start: 0.8762 (tpp) cc_final: 0.8537 (tpp) REVERT: H 80 TYR cc_start: 0.7707 (m-10) cc_final: 0.7146 (m-10) REVERT: H 82 LYS cc_start: 0.8450 (mttt) cc_final: 0.7880 (mmtt) REVERT: K 3777 MET cc_start: 0.2952 (mmp) cc_final: 0.2362 (mmp) REVERT: K 3828 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8074 (pttt) REVERT: K 3876 ASP cc_start: 0.8479 (m-30) cc_final: 0.7440 (p0) REVERT: K 3931 MET cc_start: 0.6587 (tpp) cc_final: 0.6228 (tpt) REVERT: N 226 ASP cc_start: 0.7794 (t0) cc_final: 0.7292 (t0) REVERT: N 256 LYS cc_start: 0.8486 (tppt) cc_final: 0.8165 (tppt) REVERT: N 320 ILE cc_start: 0.9023 (mp) cc_final: 0.8798 (pt) REVERT: T 500 MET cc_start: -0.0106 (ptm) cc_final: -0.1080 (ptm) REVERT: T 503 MET cc_start: 0.6124 (mmm) cc_final: 0.5697 (mpp) REVERT: R 72 TRP cc_start: 0.6363 (m100) cc_final: 0.5390 (m100) REVERT: R 140 GLN cc_start: 0.5572 (mt0) cc_final: 0.4949 (mm110) REVERT: R 230 LEU cc_start: 0.6390 (tp) cc_final: 0.5724 (tp) outliers start: 67 outliers final: 51 residues processed: 305 average time/residue: 0.3079 time to fit residues: 145.0001 Evaluate side-chains 310 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 256 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3867 GLN Chi-restraints excluded: chain K residue 3868 THR Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3919 ASN Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 212 ASP Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 307 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 175 optimal weight: 0.0270 chunk 186 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21716 Z= 0.242 Angle : 0.626 12.788 30585 Z= 0.348 Chirality : 0.041 0.189 3438 Planarity : 0.004 0.078 2870 Dihedral : 27.291 176.009 5203 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.42 % Favored : 91.53 % Rotamer: Outliers : 4.26 % Allowed : 18.87 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.19), residues: 1830 helix: 1.37 (0.22), residues: 556 sheet: -2.05 (0.29), residues: 283 loop : -2.51 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 35 HIS 0.021 0.001 HIS K3839 PHE 0.013 0.001 PHE N 206 TYR 0.026 0.002 TYR N 115 ARG 0.007 0.000 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 256 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9212 (p) cc_final: 0.8898 (p) REVERT: A 118 THR cc_start: 0.8543 (m) cc_final: 0.8172 (p) REVERT: C 56 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7231 (tp30) REVERT: C 61 GLU cc_start: 0.8694 (tp30) cc_final: 0.8474 (tp30) REVERT: D 48 ASP cc_start: 0.7007 (t0) cc_final: 0.6568 (t0) REVERT: D 54 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8931 (mmmt) REVERT: D 59 MET cc_start: 0.9058 (mmm) cc_final: 0.8835 (mmm) REVERT: F 84 MET cc_start: 0.7496 (tpp) cc_final: 0.7098 (tpp) REVERT: F 88 TYR cc_start: 0.8606 (m-10) cc_final: 0.8166 (m-10) REVERT: F 92 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8448 (ttp80) REVERT: G 84 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: G 91 GLU cc_start: 0.8413 (pm20) cc_final: 0.8179 (pm20) REVERT: H 30 ARG cc_start: 0.8439 (mpt180) cc_final: 0.7974 (mmp-170) REVERT: H 80 TYR cc_start: 0.7729 (m-10) cc_final: 0.7197 (m-10) REVERT: H 82 LYS cc_start: 0.8473 (mttt) cc_final: 0.7899 (mmtt) REVERT: K 3777 MET cc_start: 0.3085 (mmp) cc_final: 0.2458 (mmp) REVERT: K 3828 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8411 (pttt) REVERT: K 3876 ASP cc_start: 0.8499 (m-30) cc_final: 0.7503 (p0) REVERT: K 3931 MET cc_start: 0.6639 (tpp) cc_final: 0.6264 (tpt) REVERT: N 226 ASP cc_start: 0.7814 (t0) cc_final: 0.7296 (t0) REVERT: N 256 LYS cc_start: 0.8440 (tppt) cc_final: 0.8167 (tppt) REVERT: N 320 ILE cc_start: 0.9039 (mp) cc_final: 0.8808 (pt) REVERT: T 500 MET cc_start: -0.0060 (ptm) cc_final: -0.1040 (ptm) REVERT: T 503 MET cc_start: 0.6045 (mmm) cc_final: 0.5653 (mpp) REVERT: R 72 TRP cc_start: 0.6279 (m100) cc_final: 0.5373 (m100) REVERT: R 140 GLN cc_start: 0.5564 (mt0) cc_final: 0.4928 (mm110) REVERT: R 230 LEU cc_start: 0.6312 (tp) cc_final: 0.5656 (tp) outliers start: 68 outliers final: 59 residues processed: 299 average time/residue: 0.3129 time to fit residues: 144.0803 Evaluate side-chains 311 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 249 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3867 GLN Chi-restraints excluded: chain K residue 3868 THR Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3919 ASN Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain N residue 248 LEU Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 316 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 195 CYS Chi-restraints excluded: chain R residue 212 ASP Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 307 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 137 optimal weight: 0.0980 chunk 207 optimal weight: 20.0000 chunk 190 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 101 optimal weight: 30.0000 chunk 131 optimal weight: 3.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** K3867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21716 Z= 0.346 Angle : 0.695 14.664 30585 Z= 0.382 Chirality : 0.043 0.221 3438 Planarity : 0.004 0.079 2870 Dihedral : 27.482 175.910 5203 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.78 % Favored : 90.16 % Rotamer: Outliers : 4.14 % Allowed : 19.37 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.19), residues: 1830 helix: 0.98 (0.21), residues: 552 sheet: -2.05 (0.29), residues: 272 loop : -2.56 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 35 HIS 0.020 0.002 HIS K3839 PHE 0.015 0.002 PHE N 206 TYR 0.029 0.002 TYR N 115 ARG 0.007 0.001 ARG E 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 240 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9222 (p) cc_final: 0.8919 (p) REVERT: C 56 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: C 61 GLU cc_start: 0.8734 (tp30) cc_final: 0.8487 (tp30) REVERT: D 48 ASP cc_start: 0.7117 (t0) cc_final: 0.6696 (t0) REVERT: D 54 LYS cc_start: 0.9232 (mmmt) cc_final: 0.9007 (mmmt) REVERT: D 59 MET cc_start: 0.9125 (mmm) cc_final: 0.8877 (mmm) REVERT: E 83 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7297 (mmm160) REVERT: F 84 MET cc_start: 0.7497 (tpp) cc_final: 0.7119 (tpp) REVERT: F 88 TYR cc_start: 0.8682 (m-10) cc_final: 0.8207 (m-10) REVERT: F 92 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8285 (ttp80) REVERT: G 84 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: H 30 ARG cc_start: 0.8441 (mpt180) cc_final: 0.8079 (mmp80) REVERT: H 80 TYR cc_start: 0.7727 (m-10) cc_final: 0.7075 (m-10) REVERT: H 82 LYS cc_start: 0.8451 (mttt) cc_final: 0.7918 (mmtt) REVERT: K 3876 ASP cc_start: 0.8534 (m-30) cc_final: 0.7509 (p0) REVERT: K 3931 MET cc_start: 0.6792 (tpp) cc_final: 0.6369 (tpt) REVERT: N 226 ASP cc_start: 0.7763 (t0) cc_final: 0.7268 (t0) REVERT: N 256 LYS cc_start: 0.8408 (tppt) cc_final: 0.8138 (tppt) REVERT: N 320 ILE cc_start: 0.9147 (mp) cc_final: 0.8889 (pt) REVERT: R 140 GLN cc_start: 0.5743 (mt0) cc_final: 0.4952 (mm110) REVERT: R 230 LEU cc_start: 0.6275 (tp) cc_final: 0.5512 (tp) outliers start: 66 outliers final: 58 residues processed: 281 average time/residue: 0.3157 time to fit residues: 135.6868 Evaluate side-chains 299 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 238 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 3770 LEU Chi-restraints excluded: chain K residue 3838 ILE Chi-restraints excluded: chain K residue 3845 CYS Chi-restraints excluded: chain K residue 3868 THR Chi-restraints excluded: chain K residue 3896 THR Chi-restraints excluded: chain K residue 3919 ASN Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 215 ILE Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain N residue 248 LEU Chi-restraints excluded: chain N residue 252 THR Chi-restraints excluded: chain N residue 258 CYS Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain T residue 333 VAL Chi-restraints excluded: chain T residue 480 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 212 ASP Chi-restraints excluded: chain R residue 222 PHE Chi-restraints excluded: chain R residue 307 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 165 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K3907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.141914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.107144 restraints weight = 53712.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.107458 restraints weight = 31692.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.108123 restraints weight = 22963.404| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21716 Z= 0.165 Angle : 0.601 9.972 30585 Z= 0.333 Chirality : 0.040 0.187 3438 Planarity : 0.004 0.075 2870 Dihedral : 27.062 173.638 5203 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.07 % Allowed : 20.56 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.20), residues: 1830 helix: 1.64 (0.22), residues: 554 sheet: -1.81 (0.29), residues: 294 loop : -2.41 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 198 HIS 0.018 0.001 HIS K3839 PHE 0.015 0.001 PHE N 189 TYR 0.023 0.001 TYR N 115 ARG 0.009 0.000 ARG E 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4030.77 seconds wall clock time: 73 minutes 22.54 seconds (4402.54 seconds total)