Starting phenix.real_space_refine on Sun Sep 13 14:03:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u46_26330/09_2026/7u46_26330.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u46_26330/09_2026/7u46_26330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u46_26330/09_2026/7u46_26330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u46_26330/09_2026/7u46_26330.map" model { file = "/net/cci-nas-00/data/ceres_data/7u46_26330/09_2026/7u46_26330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u46_26330/09_2026/7u46_26330.cif" } resolution = 2.68 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= 0.001 sd= 0.030 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 288 5.49 5 S 16 5.16 5 C 7565 2.51 5 N 2453 2.21 5 O 3038 1.98 5 H 11015 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 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: 24375 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1503 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "B" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1307 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1573 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1458 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1539 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1589 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1458 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "K" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3451 Classifications: {'peptide': 205} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Chain: "I" Number of atoms: 4607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4607 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 4607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4607 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 4.02, per 1000 atoms: 0.16 Number of scatterers: 24375 At special positions: 0 Unit cell: (108.385, 128.092, 119.881, 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 16 16.00 P 288 15.00 O 3038 8.00 N 2453 7.00 C 7565 6.00 H 11015 1.00 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: 2.12 Conformation dependent library (CDL) restraints added in 457.4 milliseconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 11 sheets defined 69.0% alpha, 5.9% beta 139 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.604A pdb=" N GLU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.701A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.891A pdb=" N LEU A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 93 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.550A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.840A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.686A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.929A pdb=" N ARG C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.704A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.541A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.715A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.606A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 114 " --> pdb=" O TYR E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.949A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.668A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.630A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.734A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.524A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.576A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'K' and resid 2 through 15 removed outlier: 3.673A pdb=" N GLU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS K 15 " --> pdb=" O ARG K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 29 Processing helix chain 'K' and resid 32 through 39 Processing helix chain 'K' and resid 44 through 59 Processing helix chain 'K' and resid 62 through 77 removed outlier: 3.612A pdb=" N PHE K 76 " --> pdb=" O ILE K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 81 Processing helix chain 'K' and resid 100 through 116 Processing helix chain 'K' and resid 171 through 183 Processing helix chain 'K' and resid 197 through 211 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.970A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.407A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.057A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.751A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 7.070A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.146A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 120 through 126 removed outlier: 5.300A pdb=" N TYR K 151 " --> pdb=" O SER K 164 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR K 155 " --> pdb=" O TYR K 160 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR K 160 " --> pdb=" O TYR K 155 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N TRP K 83 " --> pdb=" O LEU K 193 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU K 193 " --> pdb=" O TRP K 83 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL K 85 " --> pdb=" O MET K 191 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN K 187 " --> pdb=" O SER K 89 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11012 1.03 - 1.22: 125 1.22 - 1.42: 6172 1.42 - 1.61: 7880 1.61 - 1.81: 30 Bond restraints: 25219 Sorted by residual: bond pdb=" C1' DT J 69 " pdb=" N1 DT J 69 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.43e+01 bond pdb=" C1' DT I 69 " pdb=" N1 DT I 69 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" C1' DT I 53 " pdb=" N1 DT I 53 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.06e+01 bond pdb=" C3' DC I -49 " pdb=" C2' DC I -49 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C1' DT I 70 " pdb=" N1 DT I 70 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.01e+01 ... (remaining 25214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 44364 2.19 - 4.38: 1295 4.38 - 6.57: 34 6.57 - 8.76: 8 8.76 - 10.95: 4 Bond angle restraints: 45705 Sorted by residual: angle pdb=" O4' DA J -45 " pdb=" C1' DA J -45 " pdb=" N9 DA J -45 " ideal model delta sigma weight residual 108.00 111.45 -3.45 7.00e-01 2.04e+00 2.43e+01 angle pdb=" N3 DT I -60 " pdb=" C4 DT I -60 " pdb=" O4 DT I -60 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" N3 DT J 1 " pdb=" C4 DT J 1 " pdb=" O4 DT J 1 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" N3 DT J -9 " pdb=" C4 DT J -9 " pdb=" O4 DT J -9 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" N3 DT I -4 " pdb=" C4 DT I -4 " pdb=" O4 DT I -4 " ideal model delta sigma weight residual 119.90 122.67 -2.77 6.00e-01 2.78e+00 2.13e+01 ... (remaining 45700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.26: 8823 32.26 - 64.52: 1843 64.52 - 96.78: 61 96.78 - 129.04: 2 129.04 - 161.30: 3 Dihedral angle restraints: 10732 sinusoidal: 7617 harmonic: 3115 Sorted by residual: dihedral pdb=" CA HIS F 75 " pdb=" C HIS F 75 " pdb=" N ALA F 76 " pdb=" CA ALA F 76 " ideal model delta harmonic sigma weight residual 180.00 157.48 22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA TYR B 98 " pdb=" C TYR B 98 " pdb=" N GLY B 99 " pdb=" CA GLY B 99 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DT J -22 " pdb=" C3' DT J -22 " pdb=" O3' DT J -22 " pdb=" P DC J -21 " ideal model delta sinusoidal sigma weight residual 220.00 58.70 161.30 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 10729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1671 0.069 - 0.138: 435 0.138 - 0.207: 205 0.207 - 0.275: 3 0.275 - 0.344: 2 Chirality restraints: 2316 Sorted by residual: chirality pdb=" P DC I -24 " pdb=" OP1 DC I -24 " pdb=" OP2 DC I -24 " pdb=" O5' DC I -24 " both_signs ideal model delta sigma weight residual True 2.34 -2.68 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" P DC J -24 " pdb=" OP1 DC J -24 " pdb=" OP2 DC J -24 " pdb=" O5' DC J -24 " both_signs ideal model delta sigma weight residual True 2.34 -2.64 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C3' DT J -22 " pdb=" C4' DT J -22 " pdb=" O3' DT J -22 " pdb=" C2' DT J -22 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2313 not shown) Planarity restraints: 2666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 50 " -0.028 2.00e-02 2.50e+03 2.35e-02 1.66e+01 pdb=" CG TYR G 50 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR G 50 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR G 50 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR G 50 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR G 50 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR G 50 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 50 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR G 50 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 TYR G 50 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR G 50 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR G 50 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 98 " 0.035 2.00e-02 2.50e+03 1.59e-02 7.61e+00 pdb=" CG TYR B 98 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR B 98 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 98 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 98 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 98 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 98 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 98 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 TYR B 98 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR B 98 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR B 98 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR B 98 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 122 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO E 123 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 123 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 123 " 0.032 5.00e-02 4.00e+02 ... (remaining 2663 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 959 2.17 - 2.78: 41187 2.78 - 3.38: 59937 3.38 - 3.99: 87001 3.99 - 4.60: 134856 Nonbonded interactions: 323940 Sorted by model distance: nonbonded pdb=" O4 DT I 23 " pdb=" H62 DA J -23 " model vdw 1.559 2.450 nonbonded pdb=" OD2 ASP K 70 " pdb=" HH TYR K 151 " model vdw 1.594 2.450 nonbonded pdb="HH11 ARG A 80 " pdb=" OE1 GLU K 7 " model vdw 1.627 2.450 nonbonded pdb=" HG SER K 32 " pdb=" OE1 GLN K 35 " model vdw 1.651 2.450 nonbonded pdb=" OE1 GLU E 73 " pdb="HD21 ASN F 25 " model vdw 1.655 2.450 ... (remaining 323935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 46 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 112) selection = (chain 'G' and resid 15 through 112) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72)) selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72)) } 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: 4.480 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: 0.130 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 26.120 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.012 0.090 14204 Z= 0.701 Angle : 0.939 10.948 20430 Z= 0.761 Chirality : 0.072 0.344 2316 Planarity : 0.005 0.058 1569 Dihedral : 26.919 161.305 6092 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.77 % Allowed : 0.77 % Favored : 98.47 % 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: -0.24 (0.27), residues: 905 helix: 0.57 (0.21), residues: 620 sheet: -1.15 (0.70), residues: 43 loop : -1.72 (0.32), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 69 TYR 0.065 0.003 TYR G 50 PHE 0.013 0.002 PHE H 70 TRP 0.014 0.002 TRP A 86 HIS 0.007 0.002 HIS K 186 Details of bonding type rmsd/Z covalent geometry : bond 0.01167 / 0.70 (14204) covalent geometry : angle 0.93949 / 0.76 (20430) hydrogen bonds : bond 0.15720 / 9.91 ( 799) hydrogen bonds : angle 4.55970 / 3.19 ( 2050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.7783 (ttpt) cc_final: 0.7566 (ttpt) REVERT: K 140 GLN cc_start: 0.8563 (tt0) cc_final: 0.7648 (tp-100) outliers start: 6 outliers final: 0 residues processed: 85 average time/residue: 1.6914 time to fit residues: 153.1230 Evaluate side-chains 60 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 100 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 73 ASN H 49 HIS H 63 ASN ** K 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.184552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117595 restraints weight = 32527.721| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.25 r_work: 0.3259 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14204 Z= 0.169 Angle : 0.706 8.192 20430 Z= 0.429 Chirality : 0.045 0.308 2316 Planarity : 0.005 0.050 1569 Dihedral : 30.347 164.736 4266 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.89 % Allowed : 5.87 % Favored : 93.24 % 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: 1.04 (0.27), residues: 905 helix: 1.45 (0.20), residues: 633 sheet: -0.28 (0.74), residues: 45 loop : -1.21 (0.34), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 69 TYR 0.016 0.001 TYR B 98 PHE 0.011 0.001 PHE F 61 TRP 0.006 0.001 TRP A 86 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.17 (14204) covalent geometry : angle 0.70631 / 0.43 (20430) hydrogen bonds : bond 0.06621 / 4.32 ( 799) hydrogen bonds : angle 3.31857 / 2.37 ( 2050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7582 (ttpt) REVERT: G 74 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7982 (mtmm) REVERT: K 140 GLN cc_start: 0.8730 (tt0) cc_final: 0.7729 (tp-100) outliers start: 7 outliers final: 2 residues processed: 76 average time/residue: 1.6374 time to fit residues: 132.7987 Evaluate side-chains 69 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 25 optimal weight: 0.0070 chunk 32 optimal weight: 1.9990 overall best weight: 0.8604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.182739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114748 restraints weight = 32522.935| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.25 r_work: 0.3223 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14204 Z= 0.169 Angle : 0.641 8.453 20430 Z= 0.397 Chirality : 0.041 0.302 2316 Planarity : 0.004 0.045 1569 Dihedral : 30.501 162.804 4266 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.51 % Allowed : 7.78 % Favored : 91.71 % 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: 1.60 (0.27), residues: 905 helix: 1.95 (0.21), residues: 635 sheet: -0.06 (0.74), residues: 45 loop : -1.32 (0.34), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 69 TYR 0.012 0.001 TYR B 98 PHE 0.008 0.001 PHE K 108 TRP 0.007 0.001 TRP E 86 HIS 0.010 0.001 HIS K 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.17 (14204) covalent geometry : angle 0.64064 / 0.40 (20430) hydrogen bonds : bond 0.05878 / 3.73 ( 799) hydrogen bonds : angle 3.07782 / 2.20 ( 2050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.7847 (ttpt) cc_final: 0.7640 (ttpt) REVERT: C 64 GLU cc_start: 0.7661 (tt0) cc_final: 0.7365 (tt0) REVERT: C 73 ASN cc_start: 0.6799 (m-40) cc_final: 0.6188 (t0) REVERT: C 91 GLU cc_start: 0.8523 (tt0) cc_final: 0.8304 (tm-30) REVERT: D 71 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7203 (mt-10) REVERT: G 74 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7954 (mtmm) REVERT: K 54 HIS cc_start: 0.7517 (t-90) cc_final: 0.7040 (t70) REVERT: K 140 GLN cc_start: 0.8736 (tt0) cc_final: 0.7759 (tp-100) outliers start: 4 outliers final: 3 residues processed: 79 average time/residue: 1.5634 time to fit residues: 132.2748 Evaluate side-chains 75 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 50.0000 chunk 101 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.180182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110946 restraints weight = 32405.456| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.26 r_work: 0.3172 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14204 Z= 0.180 Angle : 0.667 9.053 20430 Z= 0.401 Chirality : 0.043 0.320 2316 Planarity : 0.005 0.049 1569 Dihedral : 30.533 164.542 4266 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.77 % Allowed : 8.80 % Favored : 90.43 % 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: 1.58 (0.27), residues: 905 helix: 1.93 (0.20), residues: 637 sheet: 0.08 (0.76), residues: 45 loop : -1.40 (0.34), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 69 TYR 0.014 0.001 TYR B 98 PHE 0.008 0.001 PHE K 123 TRP 0.009 0.001 TRP E 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 (14204) covalent geometry : angle 0.66671 / 0.40 (20430) hydrogen bonds : bond 0.06047 / 3.89 ( 799) hydrogen bonds : angle 2.96025 / 2.12 ( 2050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.545 Fit side-chains REVERT: B 91 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7670 (ttpt) REVERT: C 61 GLU cc_start: 0.7258 (tp30) cc_final: 0.7049 (tp30) REVERT: C 64 GLU cc_start: 0.7785 (tt0) cc_final: 0.7509 (tt0) REVERT: G 74 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7882 (mtmm) REVERT: H 99 ARG cc_start: 0.7422 (mtt-85) cc_final: 0.7094 (mtt180) REVERT: K 54 HIS cc_start: 0.7436 (t-90) cc_final: 0.6950 (t70) REVERT: K 140 GLN cc_start: 0.8744 (tt0) cc_final: 0.7748 (tp-100) REVERT: K 191 MET cc_start: 0.7396 (tpp) cc_final: 0.6482 (mpp) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 1.6809 time to fit residues: 159.4049 Evaluate side-chains 81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 0.9990 chunk 72 optimal weight: 0.1980 chunk 89 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.180427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111048 restraints weight = 32323.366| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.25 r_work: 0.3174 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14204 Z= 0.171 Angle : 0.647 8.440 20430 Z= 0.392 Chirality : 0.041 0.296 2316 Planarity : 0.004 0.045 1569 Dihedral : 30.536 164.459 4266 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.51 % Allowed : 9.69 % Favored : 89.80 % 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: 1.73 (0.28), residues: 905 helix: 2.05 (0.20), residues: 636 sheet: 0.28 (0.76), residues: 45 loop : -1.36 (0.35), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 69 TYR 0.009 0.001 TYR F 51 PHE 0.010 0.001 PHE K 108 TRP 0.008 0.001 TRP A 86 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (14204) covalent geometry : angle 0.64737 / 0.39 (20430) hydrogen bonds : bond 0.05731 / 3.66 ( 799) hydrogen bonds : angle 2.92852 / 2.10 ( 2050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.491 Fit side-chains REVERT: B 91 LYS cc_start: 0.7885 (ttpt) cc_final: 0.7679 (ttpt) REVERT: C 61 GLU cc_start: 0.7317 (tp30) cc_final: 0.7105 (tp30) REVERT: C 64 GLU cc_start: 0.7805 (tt0) cc_final: 0.7529 (tt0) REVERT: C 73 ASN cc_start: 0.6698 (m-40) cc_final: 0.6067 (t0) REVERT: G 101 THR cc_start: 0.8519 (t) cc_final: 0.8201 (p) REVERT: K 140 GLN cc_start: 0.8759 (tt0) cc_final: 0.7756 (tp-100) outliers start: 4 outliers final: 2 residues processed: 81 average time/residue: 1.5959 time to fit residues: 138.0283 Evaluate side-chains 80 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.182902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.114256 restraints weight = 32355.696| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.21 r_work: 0.3197 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14204 Z= 0.155 Angle : 0.628 8.238 20430 Z= 0.383 Chirality : 0.041 0.303 2316 Planarity : 0.004 0.046 1569 Dihedral : 30.529 163.361 4266 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.64 % Allowed : 9.69 % Favored : 89.67 % 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: 1.94 (0.28), residues: 905 helix: 2.21 (0.21), residues: 637 sheet: 0.32 (0.78), residues: 45 loop : -1.30 (0.36), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 80 TYR 0.011 0.001 TYR F 51 PHE 0.011 0.001 PHE K 162 TRP 0.007 0.001 TRP E 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (14204) covalent geometry : angle 0.62812 / 0.38 (20430) hydrogen bonds : bond 0.05334 / 3.42 ( 799) hydrogen bonds : angle 2.85782 / 2.05 ( 2050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.7499 (tp30) cc_final: 0.7286 (tp30) REVERT: C 64 GLU cc_start: 0.7917 (tt0) cc_final: 0.7664 (tt0) REVERT: C 73 ASN cc_start: 0.6873 (m-40) cc_final: 0.6132 (t0) REVERT: G 74 LYS cc_start: 0.8248 (mtpp) cc_final: 0.8019 (mtmm) REVERT: K 54 HIS cc_start: 0.7497 (t-90) cc_final: 0.7023 (t70) REVERT: K 140 GLN cc_start: 0.8775 (tt0) cc_final: 0.7792 (tp-100) outliers start: 5 outliers final: 4 residues processed: 85 average time/residue: 1.6590 time to fit residues: 149.8438 Evaluate side-chains 85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 50.0000 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.183559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114902 restraints weight = 32354.733| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.21 r_work: 0.3210 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14204 Z= 0.150 Angle : 0.616 8.214 20430 Z= 0.376 Chirality : 0.040 0.294 2316 Planarity : 0.004 0.045 1569 Dihedral : 30.517 163.105 4266 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.64 % Allowed : 11.10 % Favored : 88.27 % 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: 2.09 (0.28), residues: 905 helix: 2.30 (0.21), residues: 639 sheet: 0.40 (0.78), residues: 45 loop : -1.23 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 169 TYR 0.009 0.001 TYR F 51 PHE 0.008 0.001 PHE K 162 TRP 0.006 0.001 TRP E 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (14204) covalent geometry : angle 0.61625 / 0.38 (20430) hydrogen bonds : bond 0.05083 / 3.25 ( 799) hydrogen bonds : angle 2.80898 / 2.01 ( 2050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7901 (tt0) cc_final: 0.7658 (tt0) REVERT: C 73 ASN cc_start: 0.6647 (m-40) cc_final: 0.5950 (t0) REVERT: K 140 GLN cc_start: 0.8773 (tt0) cc_final: 0.7770 (tp-100) outliers start: 5 outliers final: 3 residues processed: 86 average time/residue: 1.5881 time to fit residues: 145.5733 Evaluate side-chains 82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 102 optimal weight: 50.0000 chunk 105 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.183579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114751 restraints weight = 32255.484| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.22 r_work: 0.3213 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14204 Z= 0.147 Angle : 0.614 8.129 20430 Z= 0.375 Chirality : 0.040 0.298 2316 Planarity : 0.004 0.055 1569 Dihedral : 30.492 162.756 4266 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.77 % Allowed : 11.61 % Favored : 87.63 % 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: 2.16 (0.28), residues: 905 helix: 2.35 (0.21), residues: 639 sheet: 0.42 (0.79), residues: 45 loop : -1.21 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 169 TYR 0.009 0.001 TYR F 51 PHE 0.008 0.001 PHE K 41 TRP 0.006 0.001 TRP E 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (14204) covalent geometry : angle 0.61358 / 0.37 (20430) hydrogen bonds : bond 0.05020 / 3.22 ( 799) hydrogen bonds : angle 2.77977 / 1.99 ( 2050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7894 (tt0) cc_final: 0.7662 (tt0) REVERT: C 73 ASN cc_start: 0.6636 (m-40) cc_final: 0.5947 (t0) REVERT: K 140 GLN cc_start: 0.8789 (tt0) cc_final: 0.7784 (tp-100) outliers start: 6 outliers final: 5 residues processed: 88 average time/residue: 1.5995 time to fit residues: 150.8438 Evaluate side-chains 84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.183449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114724 restraints weight = 32331.519| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.21 r_work: 0.3213 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14204 Z= 0.148 Angle : 0.612 8.098 20430 Z= 0.373 Chirality : 0.040 0.296 2316 Planarity : 0.004 0.045 1569 Dihedral : 30.471 162.686 4266 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.64 % Allowed : 11.86 % Favored : 87.50 % 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: 2.20 (0.28), residues: 905 helix: 2.38 (0.20), residues: 639 sheet: 0.54 (0.80), residues: 45 loop : -1.20 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 169 TYR 0.009 0.001 TYR F 51 PHE 0.007 0.001 PHE K 162 TRP 0.007 0.001 TRP E 86 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (14204) covalent geometry : angle 0.61190 / 0.37 (20430) hydrogen bonds : bond 0.05010 / 3.21 ( 799) hydrogen bonds : angle 2.76512 / 1.98 ( 2050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7924 (tt0) cc_final: 0.7697 (tt0) REVERT: C 73 ASN cc_start: 0.6574 (m-40) cc_final: 0.5885 (t0) REVERT: K 140 GLN cc_start: 0.8790 (tt0) cc_final: 0.7749 (tp-100) outliers start: 5 outliers final: 5 residues processed: 82 average time/residue: 1.5758 time to fit residues: 138.4663 Evaluate side-chains 83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 89 optimal weight: 10.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.181905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112700 restraints weight = 32236.354| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.22 r_work: 0.3185 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14204 Z= 0.172 Angle : 0.630 8.108 20430 Z= 0.381 Chirality : 0.041 0.312 2316 Planarity : 0.004 0.046 1569 Dihedral : 30.453 162.821 4266 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.02 % Allowed : 11.48 % Favored : 87.50 % 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: 2.03 (0.28), residues: 905 helix: 2.25 (0.20), residues: 639 sheet: 0.56 (0.81), residues: 45 loop : -1.27 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 169 TYR 0.009 0.001 TYR B 51 PHE 0.008 0.001 PHE K 108 TRP 0.008 0.001 TRP E 86 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (14204) covalent geometry : angle 0.63021 / 0.38 (20430) hydrogen bonds : bond 0.05520 / 3.52 ( 799) hydrogen bonds : angle 2.79532 / 2.00 ( 2050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7897 (tt0) cc_final: 0.7665 (tt0) REVERT: C 73 ASN cc_start: 0.6686 (m-40) cc_final: 0.5997 (t0) REVERT: K 140 GLN cc_start: 0.8819 (tt0) cc_final: 0.7781 (tp-100) REVERT: K 191 MET cc_start: 0.7579 (tpp) cc_final: 0.6356 (mpp) outliers start: 8 outliers final: 6 residues processed: 83 average time/residue: 1.5505 time to fit residues: 137.6336 Evaluate side-chains 83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 10.0000 chunk 102 optimal weight: 50.0000 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.182323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113138 restraints weight = 32288.468| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.22 r_work: 0.3191 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14204 Z= 0.146 Angle : 0.621 8.069 20430 Z= 0.378 Chirality : 0.040 0.302 2316 Planarity : 0.004 0.046 1569 Dihedral : 30.448 162.646 4266 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.77 % Allowed : 11.86 % Favored : 87.37 % 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: 2.06 (0.28), residues: 905 helix: 2.27 (0.20), residues: 639 sheet: 0.57 (0.81), residues: 45 loop : -1.26 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 69 TYR 0.009 0.001 TYR F 51 PHE 0.008 0.001 PHE K 162 TRP 0.008 0.001 TRP E 86 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.15 (14204) covalent geometry : angle 0.62140 / 0.38 (20430) hydrogen bonds : bond 0.05264 / 3.36 ( 799) hydrogen bonds : angle 2.81585 / 2.02 ( 2050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8021.59 seconds wall clock time: 135 minutes 56.61 seconds (8156.61 seconds total)