Starting phenix.real_space_refine on Sat Sep 12 15:30:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ys5_10892/09_2026/6ys5_10892.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ys5_10892/09_2026/6ys5_10892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ys5_10892/09_2026/6ys5_10892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ys5_10892/09_2026/6ys5_10892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ys5_10892/09_2026/6ys5_10892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ys5_10892/09_2026/6ys5_10892.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ys5_10892/09_2026/6ys5_10892.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ys5_10892/09_2026/6ys5_10892.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 P 477 5.49 5 Mg 24 5.21 5 S 24 5.16 5 C 8718 2.51 5 N 3115 2.21 5 O 4506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16864 Number of models: 1 Model: "" Number of chains: 13 Chain: "3" Number of atoms: 9676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 9676 Classifications: {'RNAv2': 453} Modifications used: {'rna2p_pur': 35, 'rna2p_pyr': 39, 'rna3p_pur': 208, 'rna3p_pyr': 171} Link IDs: {'rna2p': 74, 'rna3p': 378} Chain breaks: 1 Chain: "7" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 428 Classifications: {'RNAv2': 20} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna3p': 19} Chain: "9" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Classifications: {'RNAv2': 4} Modifications used: {'rna3p_pyr': 4} Link IDs: {'rna3p': 3} Chain: "d" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1649 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "h" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 871 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "j" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "k" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 797 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "n" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "o" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 791 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 650 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "3" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Unusual residues: {' MG': 22} Classifications: {'undetermined': 22} Link IDs: {None: 21} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.53, per 1000 atoms: 0.21 Number of scatterers: 16864 At special positions: 0 Unit cell: (116.63, 123.05, 128.4, 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) S 24 16.00 P 477 15.00 Mg 24 11.99 O 4506 8.00 N 3115 7.00 C 8718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 265.1 milliseconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 45.8% alpha, 16.9% beta 135 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'd' and resid 8 through 12 removed outlier: 3.903A pdb=" N LEU d 12 " --> pdb=" O GLY d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 47 removed outlier: 3.534A pdb=" N GLN d 38 " --> pdb=" O LEU d 34 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL d 39 " --> pdb=" O LYS d 35 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS d 45 " --> pdb=" O GLU d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 72 through 78 removed outlier: 3.810A pdb=" N VAL d 76 " --> pdb=" O ARG d 72 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 96 removed outlier: 3.549A pdb=" N GLN d 88 " --> pdb=" O ILE d 84 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG d 89 " --> pdb=" O GLU d 85 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN d 93 " --> pdb=" O ARG d 89 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE d 94 " --> pdb=" O GLU d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 112 through 125 removed outlier: 3.523A pdb=" N VAL d 116 " --> pdb=" O ASP d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 129 through 143 removed outlier: 3.658A pdb=" N ARG d 143 " --> pdb=" O GLN d 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 160 removed outlier: 3.524A pdb=" N GLY d 159 " --> pdb=" O ARG d 156 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA d 160 " --> pdb=" O LEU d 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 156 through 160' Processing helix chain 'h' and resid 20 through 31 removed outlier: 3.884A pdb=" N ALA h 24 " --> pdb=" O SER h 20 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS h 29 " --> pdb=" O LYS h 25 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL h 30 " --> pdb=" O PHE h 26 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 53 removed outlier: 3.531A pdb=" N ALA h 39 " --> pdb=" O LYS h 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU h 52 " --> pdb=" O GLU h 48 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 70 removed outlier: 3.692A pdb=" N GLU h 63 " --> pdb=" O VAL h 59 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU h 67 " --> pdb=" O GLU h 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS h 68 " --> pdb=" O THR h 64 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL h 69 " --> pdb=" O THR h 65 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 108 Processing helix chain 'h' and resid 115 through 129 removed outlier: 3.661A pdb=" N ALA h 121 " --> pdb=" O ALA h 117 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU h 123 " --> pdb=" O ARG h 119 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU h 125 " --> pdb=" O ALA h 121 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU h 129 " --> pdb=" O LEU h 125 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 144 removed outlier: 3.525A pdb=" N MET h 144 " --> pdb=" O ASP h 140 " (cutoff:3.500A) Processing helix chain 'j' and resid 32 through 37 Processing helix chain 'j' and resid 39 through 47 removed outlier: 3.825A pdb=" N ARG j 43 " --> pdb=" O ARG j 39 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET j 44 " --> pdb=" O GLU j 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL j 45 " --> pdb=" O THR j 41 " (cutoff:3.500A) Processing helix chain 'j' and resid 47 through 53 removed outlier: 3.542A pdb=" N GLU j 51 " --> pdb=" O ARG j 47 " (cutoff:3.500A) Processing helix chain 'j' and resid 69 through 89 removed outlier: 3.671A pdb=" N ALA j 88 " --> pdb=" O ALA j 84 " (cutoff:3.500A) Processing helix chain 'j' and resid 92 through 99 Processing helix chain 'k' and resid 14 through 32 removed outlier: 3.689A pdb=" N GLN k 20 " --> pdb=" O ARG k 16 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU k 27 " --> pdb=" O GLN k 23 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR k 28 " --> pdb=" O GLU k 24 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR k 32 " --> pdb=" O THR k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 89 Processing helix chain 'n' and resid 14 through 19 Processing helix chain 'n' and resid 20 through 22 No H-bonds generated for 'chain 'n' and resid 20 through 22' Processing helix chain 'n' and resid 26 through 38 removed outlier: 3.641A pdb=" N ALA n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 44 through 48 removed outlier: 3.524A pdb=" N LEU n 48 " --> pdb=" O ILE n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 61 removed outlier: 4.126A pdb=" N ALA n 55 " --> pdb=" O ALA n 51 " (cutoff:3.500A) Processing helix chain 'n' and resid 65 through 84 removed outlier: 3.507A pdb=" N ASN n 76 " --> pdb=" O GLU n 72 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE n 77 " --> pdb=" O ILE n 73 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS n 78 " --> pdb=" O SER n 74 " (cutoff:3.500A) Processing helix chain 'n' and resid 85 through 93 Processing helix chain 'o' and resid 3 through 20 removed outlier: 3.727A pdb=" N ILE o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN o 8 " --> pdb=" O LYS o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 32 removed outlier: 3.688A pdb=" N ARG o 24 " --> pdb=" O TYR o 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 49 removed outlier: 3.676A pdb=" N MET o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 51 No H-bonds generated for 'chain 'o' and resid 50 through 51' Processing helix chain 'o' and resid 52 through 60 Proline residue: o 57 - end of helix removed outlier: 3.591A pdb=" N LEU o 60 " --> pdb=" O PRO o 57 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 90 removed outlier: 3.515A pdb=" N ASP o 86 " --> pdb=" O ASN o 82 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN o 90 " --> pdb=" O ASP o 86 " (cutoff:3.500A) Processing helix chain 't' and resid 12 through 26 removed outlier: 3.538A pdb=" N ALA t 24 " --> pdb=" O GLU t 20 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER t 25 " --> pdb=" O ALA t 21 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 75 removed outlier: 3.537A pdb=" N ALA t 75 " --> pdb=" O GLY t 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 20 through 21 removed outlier: 3.637A pdb=" N ASN d 54 " --> pdb=" O SER d 69 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA d 64 " --> pdb=" O GLN d 100 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER d 102 " --> pdb=" O ALA d 64 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL d 66 " --> pdb=" O SER d 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 165 through 171 removed outlier: 3.617A pdb=" N GLY d 148 " --> pdb=" O PHE d 203 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG d 204 " --> pdb=" O ASP d 181 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP d 181 " --> pdb=" O ARG d 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'j' and resid 4 through 7 removed outlier: 6.439A pdb=" N LYS j 25 " --> pdb=" O LEU j 61 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE j 63 " --> pdb=" O LYS j 25 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL j 27 " --> pdb=" O ILE j 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.824A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.824A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'n' and resid 3 through 4 Processing sheet with id=AA7, first strand: chain 't' and resid 31 through 33 284 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 578 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2376 1.32 - 1.45: 7110 1.45 - 1.57: 7656 1.57 - 1.69: 950 1.69 - 1.81: 45 Bond restraints: 18137 Sorted by residual: bond pdb=" CA ARG n 107 " pdb=" C ARG n 107 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.72e-02 3.38e+03 4.04e+00 bond pdb=" O3' A 31354 " pdb=" P U 31355 " ideal model delta sigma weight residual 1.607 1.586 0.021 1.20e-02 6.94e+03 2.94e+00 bond pdb=" C ALA n 106 " pdb=" N ARG n 107 " ideal model delta sigma weight residual 1.333 1.309 0.024 1.56e-02 4.11e+03 2.39e+00 bond pdb=" CG ARG j 120 " pdb=" CD ARG j 120 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.36e+00 bond pdb=" CB GLU o 14 " pdb=" CG GLU o 14 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.05e+00 ... (remaining 18132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 24147 1.50 - 3.00: 1858 3.00 - 4.50: 634 4.50 - 6.00: 165 6.00 - 7.50: 8 Bond angle restraints: 26812 Sorted by residual: angle pdb=" C PRO k 55 " pdb=" N HIS k 56 " pdb=" CA HIS k 56 " ideal model delta sigma weight residual 122.44 116.36 6.08 1.19e+00 7.06e-01 2.61e+01 angle pdb=" N HIS k 56 " pdb=" CA HIS k 56 " pdb=" C HIS k 56 " ideal model delta sigma weight residual 111.02 117.89 -6.87 1.52e+00 4.33e-01 2.04e+01 angle pdb=" C3' U 7 27 " pdb=" O3' U 7 27 " pdb=" P C 7 28 " ideal model delta sigma weight residual 119.70 124.08 -4.38 1.20e+00 6.94e-01 1.33e+01 angle pdb=" CA ARG n 107 " pdb=" C ARG n 107 " pdb=" N THR n 108 " ideal model delta sigma weight residual 118.59 124.29 -5.70 1.63e+00 3.76e-01 1.22e+01 angle pdb=" O3' A 31198 " pdb=" C3' A 31198 " pdb=" C2' A 31198 " ideal model delta sigma weight residual 113.80 107.61 6.19 2.00e+00 2.50e-01 9.58e+00 ... (remaining 26807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.55: 8309 23.55 - 47.10: 1034 47.10 - 70.66: 485 70.66 - 94.21: 75 94.21 - 117.76: 1 Dihedral angle restraints: 9904 sinusoidal: 7468 harmonic: 2436 Sorted by residual: dihedral pdb=" C4' G 31050 " pdb=" C3' G 31050 " pdb=" C2' G 31050 " pdb=" C1' G 31050 " ideal model delta sinusoidal sigma weight residual 36.34 -40.00 76.35 1 3.10e+00 1.04e-01 7.63e+02 dihedral pdb=" C4' C 31211 " pdb=" C3' C 31211 " pdb=" C2' C 31211 " pdb=" C1' C 31211 " ideal model delta sinusoidal sigma weight residual 36.34 -39.77 76.11 1 3.10e+00 1.04e-01 7.59e+02 dihedral pdb=" C4' U 3 957 " pdb=" C3' U 3 957 " pdb=" C2' U 3 957 " pdb=" C1' U 3 957 " ideal model delta sinusoidal sigma weight residual 36.34 -39.51 75.85 1 3.10e+00 1.04e-01 7.55e+02 ... (remaining 9901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2330 0.064 - 0.128: 412 0.128 - 0.192: 145 0.192 - 0.255: 398 0.255 - 0.319: 128 Chirality restraints: 3413 Sorted by residual: chirality pdb=" C2' U 3 957 " pdb=" C3' U 3 957 " pdb=" O2' U 3 957 " pdb=" C1' U 3 957 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C2' G 31172 " pdb=" C3' G 31172 " pdb=" O2' G 31172 " pdb=" C1' G 31172 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" P U 31083 " pdb=" OP1 U 31083 " pdb=" OP2 U 31083 " pdb=" O5' U 31083 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 3410 not shown) Planarity restraints: 1645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 3 955 " 0.047 2.00e-02 2.50e+03 2.20e-02 1.33e+01 pdb=" N9 A 3 955 " -0.052 2.00e-02 2.50e+03 pdb=" C8 A 3 955 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A 3 955 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 3 955 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A 3 955 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A 3 955 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A 3 955 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A 3 955 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A 3 955 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A 3 955 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 31354 " -0.042 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" N9 A 31354 " 0.045 2.00e-02 2.50e+03 pdb=" C8 A 31354 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 31354 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A 31354 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A 31354 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A 31354 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A 31354 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A 31354 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 31354 " 0.011 2.00e-02 2.50e+03 pdb=" C4 A 31354 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 31353 " -0.038 2.00e-02 2.50e+03 1.71e-02 8.82e+00 pdb=" N9 G 31353 " 0.041 2.00e-02 2.50e+03 pdb=" C8 G 31353 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G 31353 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 31353 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G 31353 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G 31353 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G 31353 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G 31353 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G 31353 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G 31353 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 31353 " 0.001 2.00e-02 2.50e+03 ... (remaining 1642 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 59 2.48 - 3.09: 10419 3.09 - 3.69: 28528 3.69 - 4.30: 45757 4.30 - 4.90: 62981 Nonbonded interactions: 147744 Sorted by model distance: nonbonded pdb=" O6 G 31105 " pdb="MG MG 31608 " model vdw 1.880 2.170 nonbonded pdb=" OP1 U 31196 " pdb="MG MG 31606 " model vdw 1.981 2.170 nonbonded pdb=" O LYS h 114 " pdb=" NH1 ARG h 119 " model vdw 2.056 3.120 nonbonded pdb=" OP2 G 31301 " pdb="MG MG 31620 " model vdw 2.056 2.170 nonbonded pdb=" OP1 G 3 990 " pdb="MG MG 31614 " model vdw 2.064 2.170 ... (remaining 147739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.320 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 18137 Z= 0.365 Angle : 1.027 7.502 26812 Z= 0.445 Chirality : 0.108 0.319 3413 Planarity : 0.005 0.042 1645 Dihedral : 20.877 117.760 8330 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 7.15 % Allowed : 18.10 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.24), residues: 836 helix: -2.42 (0.22), residues: 344 sheet: 0.17 (0.44), residues: 125 loop : -2.42 (0.26), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG j 107 TYR 0.014 0.002 TYR d 29 PHE 0.012 0.002 PHE d 42 TRP 0.018 0.003 TRP o 101 HIS 0.007 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.37 (18137) covalent geometry : angle 1.02653 / 0.44 (26812) hydrogen bonds : bond 0.12427 / 6.46 ( 621) hydrogen bonds : angle 4.68476 / 1.90 ( 1391) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.375 Fit side-chains REVERT: d 11 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8635 (ptp-170) REVERT: d 110 ASP cc_start: 0.8014 (m-30) cc_final: 0.7761 (m-30) REVERT: d 152 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: d 187 MET cc_start: 0.8303 (mmm) cc_final: 0.7661 (tpt) REVERT: h 3 ARG cc_start: 0.6482 (mtm-85) cc_final: 0.6223 (mtm-85) REVERT: h 10 ARG cc_start: 0.7570 (ttm110) cc_final: 0.7360 (ttm110) REVERT: h 62 PHE cc_start: 0.8326 (t80) cc_final: 0.8018 (t80) REVERT: j 40 GLU cc_start: 0.7674 (pp20) cc_final: 0.7391 (pp20) REVERT: k 47 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7275 (pt0) REVERT: n 79 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7223 (ttm110) REVERT: n 107 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7649 (mmp80) REVERT: o 85 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8081 (ttt180) outliers start: 49 outliers final: 26 residues processed: 204 average time/residue: 0.7015 time to fit residues: 157.1735 Evaluate side-chains 182 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 11 ARG Chi-restraints excluded: chain d residue 34 LEU Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 93 ASN Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 97 THR Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 50 LEU Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 56 THR Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 107 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 85 ARG Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.0070 chunk 129 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 6 HIS d 54 ASN d 104 ASN d 176 HIS h 29 HIS j 4 ASN j 30 ASN j 35 GLN j 73 GLN j 79 HIS j 124 GLN k 15 HIS k 50 ASN k 58 ASN k 64 GLN k 99 GLN n 76 ASN n 105 ASN o 8 ASN o 71 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105860 restraints weight = 20540.056| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 0.76 r_work: 0.2873 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18137 Z= 0.194 Angle : 1.291 18.643 26812 Z= 0.516 Chirality : 0.120 1.181 3413 Planarity : 0.005 0.038 1645 Dihedral : 18.127 159.366 6721 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.80 % Allowed : 24.23 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.27), residues: 836 helix: -0.92 (0.27), residues: 337 sheet: 0.94 (0.46), residues: 123 loop : -1.99 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 72 TYR 0.009 0.001 TYR d 29 PHE 0.010 0.001 PHE d 42 TRP 0.013 0.002 TRP o 101 HIS 0.007 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (18137) covalent geometry : angle 1.29139 / 0.52 (26812) hydrogen bonds : bond 0.06126 / 3.45 ( 621) hydrogen bonds : angle 3.54330 / 1.46 ( 1391) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.419 Fit side-chains REVERT: h 10 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7588 (ttm110) REVERT: j 27 VAL cc_start: 0.9081 (m) cc_final: 0.8858 (t) REVERT: k 85 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: n 79 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7856 (ttm110) outliers start: 26 outliers final: 18 residues processed: 184 average time/residue: 0.6612 time to fit residues: 134.6785 Evaluate side-chains 173 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 110 ASP Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 110 LYS Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 3 GLN h 54 ASN k 64 GLN k 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.104981 restraints weight = 20732.022| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.15 r_work: 0.2697 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 18137 Z= 0.341 Angle : 1.337 19.512 26812 Z= 0.536 Chirality : 0.123 1.540 3413 Planarity : 0.006 0.046 1645 Dihedral : 18.212 175.033 6675 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 6.13 % Allowed : 24.38 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.28), residues: 836 helix: -0.66 (0.27), residues: 346 sheet: 1.04 (0.46), residues: 128 loop : -1.86 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG h 119 TYR 0.012 0.002 TYR d 29 PHE 0.012 0.002 PHE t 74 TRP 0.016 0.002 TRP o 101 HIS 0.005 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.34 (18137) covalent geometry : angle 1.33666 / 0.54 (26812) hydrogen bonds : bond 0.06758 / 3.65 ( 621) hydrogen bonds : angle 3.57856 / 1.47 ( 1391) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.392 Fit side-chains REVERT: d 136 ARG cc_start: 0.8545 (ttm170) cc_final: 0.8321 (ttm170) REVERT: d 140 ASN cc_start: 0.8889 (t0) cc_final: 0.8609 (t0) REVERT: d 152 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: d 187 MET cc_start: 0.9000 (mmm) cc_final: 0.8440 (tpt) REVERT: h 5 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.5321 (mmt90) REVERT: h 10 ARG cc_start: 0.8331 (ttm110) cc_final: 0.7754 (ttm110) REVERT: h 52 GLU cc_start: 0.7553 (pt0) cc_final: 0.7335 (pt0) REVERT: j 26 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8668 (tt) REVERT: j 40 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7723 (tm-30) REVERT: k 47 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: k 85 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: n 71 ARG cc_start: 0.8139 (mtm110) cc_final: 0.7838 (ttm-80) REVERT: n 78 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7983 (mtpp) REVERT: n 79 ARG cc_start: 0.8114 (ttm110) cc_final: 0.7843 (ttm110) outliers start: 42 outliers final: 27 residues processed: 180 average time/residue: 0.6914 time to fit residues: 137.3594 Evaluate side-chains 181 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 110 LYS Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 56 THR Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 78 LYS Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 103 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 96 optimal weight: 0.0670 chunk 102 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... k 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.110922 restraints weight = 20824.940| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 0.71 r_work: 0.2959 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18137 Z= 0.161 Angle : 1.064 13.668 26812 Z= 0.424 Chirality : 0.092 0.857 3413 Planarity : 0.004 0.037 1645 Dihedral : 17.946 179.345 6675 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.67 % Allowed : 25.84 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.28), residues: 836 helix: 0.00 (0.29), residues: 339 sheet: 1.48 (0.48), residues: 123 loop : -1.57 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG h 119 TYR 0.007 0.001 TYR j 5 PHE 0.012 0.001 PHE h 61 TRP 0.013 0.002 TRP o 101 HIS 0.002 0.001 HIS t 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (18137) covalent geometry : angle 1.06366 / 0.42 (26812) hydrogen bonds : bond 0.05992 / 3.33 ( 621) hydrogen bonds : angle 3.23158 / 1.33 ( 1391) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.386 Fit side-chains REVERT: d 27 LYS cc_start: 0.8927 (ptmt) cc_final: 0.8640 (ttpt) REVERT: d 152 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: d 166 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7021 (mm-30) REVERT: h 5 ARG cc_start: 0.6172 (OUTLIER) cc_final: 0.5670 (mmt90) REVERT: h 10 ARG cc_start: 0.8015 (ttm110) cc_final: 0.7304 (ttm110) REVERT: h 27 MET cc_start: 0.8174 (ptm) cc_final: 0.7964 (mtp) REVERT: h 48 GLU cc_start: 0.6913 (pt0) cc_final: 0.6382 (pm20) REVERT: h 52 GLU cc_start: 0.7594 (pt0) cc_final: 0.7344 (pt0) REVERT: j 40 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7784 (tm-30) REVERT: k 47 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: k 60 ASP cc_start: 0.8859 (m-30) cc_final: 0.8545 (m-30) REVERT: k 85 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: n 79 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7719 (ttm170) REVERT: n 93 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7985 (mtt-85) REVERT: o 49 GLN cc_start: 0.9309 (pt0) cc_final: 0.9087 (pt0) outliers start: 32 outliers final: 16 residues processed: 183 average time/residue: 0.6935 time to fit residues: 140.1052 Evaluate side-chains 172 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 93 ARG Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 113 optimal weight: 0.9980 chunk 49 optimal weight: 0.0470 chunk 98 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 139 GLN k 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.137879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108488 restraints weight = 20570.946| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 0.79 r_work: 0.2904 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18137 Z= 0.181 Angle : 1.086 15.453 26812 Z= 0.433 Chirality : 0.095 0.962 3413 Planarity : 0.005 0.044 1645 Dihedral : 17.884 178.200 6671 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.11 % Allowed : 25.99 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.29), residues: 836 helix: 0.20 (0.29), residues: 345 sheet: 1.47 (0.46), residues: 138 loop : -1.43 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG k 31 TYR 0.008 0.001 TYR k 70 PHE 0.014 0.001 PHE h 61 TRP 0.013 0.002 TRP o 101 HIS 0.003 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (18137) covalent geometry : angle 1.08620 / 0.43 (26812) hydrogen bonds : bond 0.05757 / 3.17 ( 621) hydrogen bonds : angle 3.18285 / 1.30 ( 1391) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.359 Fit side-chains REVERT: d 27 LYS cc_start: 0.8909 (ptmt) cc_final: 0.8665 (ttpt) REVERT: d 152 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: d 166 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7016 (mm-30) REVERT: h 5 ARG cc_start: 0.6317 (OUTLIER) cc_final: 0.5436 (mmt90) REVERT: j 40 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7911 (tm-30) REVERT: j 51 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7812 (pp20) REVERT: k 47 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: k 60 ASP cc_start: 0.8878 (m-30) cc_final: 0.8573 (m-30) REVERT: k 85 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: n 8 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7411 (m110) REVERT: n 79 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7796 (ttm170) outliers start: 35 outliers final: 22 residues processed: 172 average time/residue: 0.6941 time to fit residues: 131.3061 Evaluate side-chains 176 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 8 ASN Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 128 optimal weight: 0.2980 chunk 120 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 139 GLN k 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.108194 restraints weight = 20596.830| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.16 r_work: 0.2764 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18137 Z= 0.252 Angle : 1.186 18.396 26812 Z= 0.475 Chirality : 0.105 1.235 3413 Planarity : 0.005 0.037 1645 Dihedral : 17.981 177.636 6671 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.99 % Allowed : 27.01 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.29), residues: 836 helix: 0.15 (0.29), residues: 345 sheet: 1.43 (0.45), residues: 138 loop : -1.48 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG k 31 TYR 0.010 0.002 TYR o 73 PHE 0.018 0.002 PHE h 61 TRP 0.013 0.002 TRP o 101 HIS 0.005 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.25 (18137) covalent geometry : angle 1.18612 / 0.47 (26812) hydrogen bonds : bond 0.06101 / 3.36 ( 621) hydrogen bonds : angle 3.33086 / 1.37 ( 1391) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.350 Fit side-chains REVERT: d 93 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8283 (t0) REVERT: d 152 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8416 (tm-30) REVERT: h 5 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.5162 (mmt90) REVERT: h 10 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7658 (ttm110) REVERT: h 48 GLU cc_start: 0.6954 (pt0) cc_final: 0.6404 (pm20) REVERT: j 26 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8455 (tt) REVERT: j 40 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8045 (tm-30) REVERT: j 51 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8006 (pp20) REVERT: k 47 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7742 (pt0) REVERT: k 85 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: n 3 ARG cc_start: 0.7353 (ttm-80) cc_final: 0.6702 (ttm-80) REVERT: n 8 ASN cc_start: 0.7870 (OUTLIER) cc_final: 0.7208 (m-40) REVERT: n 79 ARG cc_start: 0.8381 (ttm110) cc_final: 0.8045 (ttm170) REVERT: n 93 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8264 (mtt-85) REVERT: n 113 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7269 (mtt180) outliers start: 41 outliers final: 28 residues processed: 168 average time/residue: 0.6566 time to fit residues: 122.2585 Evaluate side-chains 175 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 93 ASN Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 110 ASP Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 8 ASN Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 93 ARG Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 105 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 139 GLN k 64 GLN k 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.108410 restraints weight = 20440.609| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.17 r_work: 0.2773 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18137 Z= 0.252 Angle : 1.176 17.649 26812 Z= 0.471 Chirality : 0.103 1.184 3413 Planarity : 0.005 0.039 1645 Dihedral : 18.084 179.662 6671 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 6.72 % Allowed : 27.01 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.29), residues: 836 helix: 0.23 (0.29), residues: 343 sheet: 1.40 (0.45), residues: 138 loop : -1.40 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG k 31 TYR 0.009 0.002 TYR o 73 PHE 0.021 0.002 PHE h 61 TRP 0.013 0.002 TRP o 101 HIS 0.005 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.25 (18137) covalent geometry : angle 1.17611 / 0.47 (26812) hydrogen bonds : bond 0.06044 / 3.33 ( 621) hydrogen bonds : angle 3.30717 / 1.36 ( 1391) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.427 Fit side-chains REVERT: d 82 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.6067 (pm20) REVERT: d 93 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8286 (t0) REVERT: d 136 ARG cc_start: 0.8730 (ttm170) cc_final: 0.8474 (ttm170) REVERT: d 152 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8413 (tm-30) REVERT: d 166 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: h 3 ARG cc_start: 0.7333 (ttp-110) cc_final: 0.7097 (ttp-110) REVERT: h 5 ARG cc_start: 0.6416 (OUTLIER) cc_final: 0.5124 (mmt90) REVERT: h 10 ARG cc_start: 0.8294 (ttm110) cc_final: 0.7650 (ttm110) REVERT: h 48 GLU cc_start: 0.6970 (pt0) cc_final: 0.6411 (pm20) REVERT: h 68 LYS cc_start: 0.7884 (tppt) cc_final: 0.7293 (tptm) REVERT: j 40 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8056 (tm-30) REVERT: j 51 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8013 (pp20) REVERT: k 47 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7743 (pt0) REVERT: k 85 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: n 3 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.7172 (ttm-80) REVERT: n 8 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7681 (m-40) REVERT: n 79 ARG cc_start: 0.8383 (ttm110) cc_final: 0.8041 (ttm170) REVERT: n 113 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7291 (mtt180) REVERT: o 85 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8187 (ttt180) outliers start: 46 outliers final: 30 residues processed: 167 average time/residue: 0.6649 time to fit residues: 122.7380 Evaluate side-chains 179 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 51 MET Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 76 VAL Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 93 ASN Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 8 ASN Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 85 ARG Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 139 GLN k 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.107268 restraints weight = 20636.806| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.16 r_work: 0.2761 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 18137 Z= 0.264 Angle : 1.193 17.922 26812 Z= 0.478 Chirality : 0.105 1.146 3413 Planarity : 0.005 0.040 1645 Dihedral : 18.098 179.905 6671 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 7.59 % Allowed : 25.40 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.29), residues: 836 helix: 0.18 (0.28), residues: 348 sheet: 1.38 (0.45), residues: 138 loop : -1.40 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 31 TYR 0.010 0.002 TYR o 73 PHE 0.021 0.002 PHE h 61 TRP 0.013 0.002 TRP o 101 HIS 0.005 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.26 (18137) covalent geometry : angle 1.19275 / 0.48 (26812) hydrogen bonds : bond 0.06119 / 3.36 ( 621) hydrogen bonds : angle 3.32665 / 1.36 ( 1391) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 142 time to evaluate : 0.279 Fit side-chains REVERT: d 136 ARG cc_start: 0.8741 (ttm170) cc_final: 0.8496 (ttp-170) REVERT: d 152 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: d 166 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: h 3 ARG cc_start: 0.7329 (ttp-110) cc_final: 0.7099 (ttp-110) REVERT: h 5 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.5100 (mmt90) REVERT: h 10 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7662 (ttm110) REVERT: h 68 LYS cc_start: 0.7938 (tppt) cc_final: 0.7320 (tptm) REVERT: j 26 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8561 (tt) REVERT: j 40 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8043 (tm-30) REVERT: j 51 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8000 (pp20) REVERT: k 47 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7717 (pt0) REVERT: k 85 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: n 8 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7618 (m-40) REVERT: n 79 ARG cc_start: 0.8352 (ttm110) cc_final: 0.8008 (ttm170) REVERT: n 93 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8239 (mtt-85) REVERT: n 113 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7277 (mtt180) REVERT: o 85 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8172 (ttt180) REVERT: t 63 THR cc_start: 0.9229 (m) cc_final: 0.8999 (m) outliers start: 52 outliers final: 34 residues processed: 176 average time/residue: 0.6747 time to fit residues: 130.9675 Evaluate side-chains 185 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 51 MET Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 76 VAL Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 8 ASN Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 72 GLU Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 93 ARG Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 38 ASP Chi-restraints excluded: chain o residue 85 ARG Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 92 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 139 GLN k 64 GLN k 99 GLN t 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.104874 restraints weight = 20545.513| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 0.74 r_work: 0.2878 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18137 Z= 0.180 Angle : 1.119 17.262 26812 Z= 0.448 Chirality : 0.097 0.968 3413 Planarity : 0.005 0.038 1645 Dihedral : 18.093 177.917 6671 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 5.55 % Allowed : 27.88 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.29), residues: 836 helix: 0.37 (0.29), residues: 346 sheet: 1.45 (0.46), residues: 138 loop : -1.30 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG k 31 TYR 0.009 0.001 TYR j 59 PHE 0.021 0.001 PHE h 61 TRP 0.013 0.002 TRP o 101 HIS 0.003 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (18137) covalent geometry : angle 1.11927 / 0.45 (26812) hydrogen bonds : bond 0.05728 / 3.18 ( 621) hydrogen bonds : angle 3.28788 / 1.36 ( 1391) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.415 Fit side-chains REVERT: d 152 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: d 166 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7433 (mm-30) REVERT: h 3 ARG cc_start: 0.7081 (ttp-110) cc_final: 0.6847 (ttp-110) REVERT: h 5 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.4881 (mmt90) REVERT: h 10 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7527 (ttm110) REVERT: h 48 GLU cc_start: 0.6848 (pt0) cc_final: 0.6332 (pm20) REVERT: h 68 LYS cc_start: 0.7874 (tppt) cc_final: 0.7320 (tptm) REVERT: j 40 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7922 (tm-30) REVERT: j 51 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7827 (pp20) REVERT: k 47 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7572 (pt0) REVERT: k 85 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: n 3 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.6978 (ttm-80) REVERT: n 79 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7787 (ttm170) REVERT: n 113 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7233 (mtt180) outliers start: 38 outliers final: 26 residues processed: 166 average time/residue: 0.6555 time to fit residues: 120.2505 Evaluate side-chains 171 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 76 VAL Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 94 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 115 optimal weight: 0.0980 chunk 110 optimal weight: 0.0030 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 123 GLN d 139 GLN k 64 GLN k 99 GLN t 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.104688 restraints weight = 20394.074| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 0.78 r_work: 0.2871 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18137 Z= 0.192 Angle : 1.112 18.657 26812 Z= 0.446 Chirality : 0.096 0.903 3413 Planarity : 0.005 0.040 1645 Dihedral : 18.038 178.235 6671 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.69 % Allowed : 27.74 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.29), residues: 836 helix: 0.45 (0.29), residues: 347 sheet: 1.52 (0.46), residues: 138 loop : -1.26 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG k 31 TYR 0.010 0.001 TYR j 59 PHE 0.021 0.001 PHE h 61 TRP 0.013 0.002 TRP o 101 HIS 0.004 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (18137) covalent geometry : angle 1.11151 / 0.45 (26812) hydrogen bonds : bond 0.05852 / 3.24 ( 621) hydrogen bonds : angle 3.22906 / 1.33 ( 1391) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.382 Fit side-chains REVERT: d 27 LYS cc_start: 0.8906 (ptmt) cc_final: 0.8673 (ttpt) REVERT: d 152 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: d 166 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7389 (mm-30) REVERT: h 10 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7457 (ttm110) REVERT: h 48 GLU cc_start: 0.6909 (pt0) cc_final: 0.6410 (pm20) REVERT: h 68 LYS cc_start: 0.7880 (tppt) cc_final: 0.7347 (tptm) REVERT: j 40 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7878 (tm-30) REVERT: j 51 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7758 (pp20) REVERT: k 47 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: k 60 ASP cc_start: 0.8885 (m-30) cc_final: 0.8551 (m-30) REVERT: k 85 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: n 79 ARG cc_start: 0.8070 (ttm110) cc_final: 0.7735 (ttm170) REVERT: n 113 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7207 (mtt180) outliers start: 39 outliers final: 30 residues processed: 164 average time/residue: 0.6853 time to fit residues: 124.2017 Evaluate side-chains 173 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 76 VAL Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 166 GLU Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 85 ASP Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 72 GLU Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Chi-restraints excluded: chain t residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 72 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 115 optimal weight: 0.0470 chunk 14 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... d 123 GLN d 139 GLN k 99 GLN n 8 ASN t 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.105777 restraints weight = 20428.512| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 0.70 r_work: 0.2868 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18137 Z= 0.176 Angle : 1.199 59.189 26812 Z= 0.529 Chirality : 0.096 0.895 3413 Planarity : 0.005 0.040 1645 Dihedral : 18.038 178.188 6671 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.96 % Allowed : 28.61 % Favored : 66.42 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.29), residues: 836 helix: 0.42 (0.29), residues: 347 sheet: 1.52 (0.46), residues: 138 loop : -1.25 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG k 31 TYR 0.008 0.001 TYR j 59 PHE 0.020 0.001 PHE h 61 TRP 0.013 0.002 TRP o 101 HIS 0.004 0.001 HIS k 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (18137) covalent geometry : angle 1.19919 / 0.53 (26812) hydrogen bonds : bond 0.05795 / 3.21 ( 621) hydrogen bonds : angle 3.24230 / 1.33 ( 1391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5141.72 seconds wall clock time: 88 minutes 29.25 seconds (5309.25 seconds total)