Starting phenix.real_space_refine on Sun Aug 9 02:52:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zqb_74563/08_2026/9zqb_74563.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zqb_74563/08_2026/9zqb_74563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zqb_74563/08_2026/9zqb_74563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zqb_74563/08_2026/9zqb_74563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zqb_74563/08_2026/9zqb_74563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zqb_74563/08_2026/9zqb_74563.map" } resolution = 2.1 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= 0.012 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 306 5.49 5 S 40 5.16 5 C 9799 2.51 5 N 3128 2.21 5 O 3833 1.98 5 H 14529 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31635 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1708 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1730 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "C" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1605 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "D" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1605 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1695 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1673 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "G" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1437 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "H" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1437 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "I" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3559 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 220} Chain breaks: 1 Chain: "J" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3559 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 220} Chain breaks: 1 Chain: "K" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1489 Classifications: {'DNA': 47} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 46} Chain: "L" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 3345 Classifications: {'DNA': 106} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 105} Chain: "M" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 4874 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "P" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1919 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Time building chain proxies: 5.08, per 1000 atoms: 0.16 Number of scatterers: 31635 At special positions: 0 Unit cell: (140.76, 127.512, 148.212, 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 40 16.00 P 306 15.00 O 3833 8.00 N 3128 7.00 C 9799 6.00 H 14529 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS I 47 " - pdb=" SG CYS I 112 " distance=2.03 Simple disulfide: pdb=" SG CYS J 47 " - pdb=" SG CYS J 112 " distance=2.04 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: 2.62 Conformation dependent library (CDL) restraints added in 774.0 milliseconds 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 26 sheets defined 45.5% alpha, 22.9% beta 153 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 5.47 Creating SS restraints... Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 45 through 73 removed outlier: 4.192A pdb=" N VAL A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'B' and resid 16 through 22 Processing helix chain 'B' and resid 26 through 37 Processing helix chain 'B' and resid 45 through 73 removed outlier: 4.230A pdb=" N VAL B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 90 through 97 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 54 through 83 Processing helix chain 'C' and resid 89 through 101 Processing helix chain 'C' and resid 102 through 123 removed outlier: 3.792A pdb=" N ALA C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 54 through 83 Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 102 through 123 removed outlier: 3.732A pdb=" N ALA D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.962A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 45 through 58 Processing helix chain 'F' and resid 64 through 77 Processing helix chain 'F' and resid 86 through 115 Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'G' and resid 26 through 31 Processing helix chain 'G' and resid 32 through 43 Processing helix chain 'G' and resid 51 through 78 removed outlier: 3.702A pdb=" N GLU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP G 70 " --> pdb=" O ASN G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 95 Processing helix chain 'H' and resid 26 through 31 Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 51 through 78 removed outlier: 3.673A pdb=" N GLU H 55 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 95 Processing helix chain 'I' and resid 103 through 107 Processing helix chain 'I' and resid 182 through 184 No H-bonds generated for 'chain 'I' and resid 182 through 184' Processing helix chain 'I' and resid 216 through 219 Processing helix chain 'I' and resid 241 through 245 Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 182 through 184 No H-bonds generated for 'chain 'J' and resid 182 through 184' Processing helix chain 'J' and resid 228 through 230 No H-bonds generated for 'chain 'J' and resid 228 through 230' Processing helix chain 'J' and resid 241 through 245 Processing helix chain 'P' and resid 124 through 127 Processing helix chain 'P' and resid 168 through 185 Processing helix chain 'P' and resid 187 through 194 removed outlier: 5.425A pdb=" N GLU P 192 " --> pdb=" O GLU P 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 7.173A pdb=" N ARG A 42 " --> pdb=" O ILE C 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.800A pdb=" N THR A 101 " --> pdb=" O TYR G 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 removed outlier: 7.129A pdb=" N ARG B 42 " --> pdb=" O ILE D 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.641A pdb=" N THR B 101 " --> pdb=" O TYR H 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.782A pdb=" N ARG E 84 " --> pdb=" O VAL G 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.722A pdb=" N ARG F 84 " --> pdb=" O VAL H 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 119 through 120 Processing sheet with id=AB2, first strand: chain 'I' and resid 28 through 31 removed outlier: 3.534A pdb=" N ASP I 94 " --> pdb=" O SER I 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.424A pdb=" N TRP I 59 " --> pdb=" O LEU I 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 34 through 37 Processing sheet with id=AB5, first strand: chain 'I' and resid 157 through 160 Processing sheet with id=AB6, first strand: chain 'I' and resid 164 through 166 removed outlier: 6.421A pdb=" N GLU I 164 " --> pdb=" O THR I 271 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE I 188 " --> pdb=" O TYR I 204 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR I 204 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP I 190 " --> pdb=" O ILE I 202 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 164 through 166 removed outlier: 6.421A pdb=" N GLU I 164 " --> pdb=" O THR I 271 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR I 263 " --> pdb=" O ARG I 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 172 through 174 Processing sheet with id=AB9, first strand: chain 'J' and resid 28 through 31 removed outlier: 3.623A pdb=" N ASP J 94 " --> pdb=" O SER J 91 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.556A pdb=" N LEU J 57 " --> pdb=" O TYR J 73 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR J 73 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP J 59 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 34 through 38 Processing sheet with id=AC3, first strand: chain 'J' and resid 157 through 160 Processing sheet with id=AC4, first strand: chain 'J' and resid 164 through 166 removed outlier: 6.474A pdb=" N ILE J 188 " --> pdb=" O TYR J 204 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR J 204 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TRP J 190 " --> pdb=" O ILE J 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 164 through 166 removed outlier: 3.909A pdb=" N TYR J 263 " --> pdb=" O ARG J 252 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 105 through 107 removed outlier: 5.480A pdb=" N PHE P 145 " --> pdb=" O CYS P 165 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 105 through 107 Processing sheet with id=AC8, first strand: chain 'P' and resid 109 through 110 633 hydrogen bonds defined for protein. 1719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 392 hydrogen bonds 784 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 8.86 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14522 1.03 - 1.23: 168 1.23 - 1.42: 8142 1.42 - 1.62: 9683 1.62 - 1.81: 69 Bond restraints: 32584 Sorted by residual: bond pdb=" C3' DC L 67 " pdb=" O3' DC L 67 " ideal model delta sigma weight residual 1.435 1.397 0.038 1.30e-02 5.92e+03 8.49e+00 bond pdb=" C3' DT M 10 " pdb=" C2' DT M 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.12e+00 bond pdb=" C3' DG L 57 " pdb=" O3' DG L 57 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.33e+00 bond pdb=" C3' DG M 104 " pdb=" O3' DG M 104 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.06e+00 bond pdb=" C3' DC L 22 " pdb=" C2' DC L 22 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.85e+00 ... (remaining 32579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 57772 2.11 - 4.23: 1133 4.23 - 6.34: 40 6.34 - 8.46: 3 8.46 - 10.57: 7 Bond angle restraints: 58955 Sorted by residual: angle pdb=" N3 DT L 68 " pdb=" C4 DT L 68 " pdb=" O4 DT L 68 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT L 101 " pdb=" C4 DT L 101 " pdb=" O4 DT L 101 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT M 34 " pdb=" C4 DT M 34 " pdb=" O4 DT M 34 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" CB ARG I 132 " pdb=" CG ARG I 132 " pdb=" CD ARG I 132 " ideal model delta sigma weight residual 111.30 120.99 -9.69 2.30e+00 1.89e-01 1.78e+01 angle pdb=" N3 DT L 98 " pdb=" C4 DT L 98 " pdb=" O4 DT L 98 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 ... (remaining 58950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.13: 12076 33.13 - 66.25: 1951 66.25 - 99.38: 42 99.38 - 132.50: 0 132.50 - 165.63: 3 Dihedral angle restraints: 14072 sinusoidal: 9510 harmonic: 4562 Sorted by residual: dihedral pdb=" C4' DG L 84 " pdb=" C3' DG L 84 " pdb=" O3' DG L 84 " pdb=" P DT L 85 " ideal model delta sinusoidal sigma weight residual 220.00 54.37 165.63 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG L 50 " pdb=" C3' DG L 50 " pdb=" O3' DG L 50 " pdb=" P DC L 51 " ideal model delta sinusoidal sigma weight residual 220.00 61.99 158.01 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DG M 97 " pdb=" C3' DG M 97 " pdb=" O3' DG M 97 " pdb=" P DG M 98 " ideal model delta sinusoidal sigma weight residual 220.00 62.37 157.63 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 14069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2444 0.082 - 0.164: 374 0.164 - 0.246: 46 0.246 - 0.328: 0 0.328 - 0.410: 2 Chirality restraints: 2866 Sorted by residual: chirality pdb=" P DA M 4 " pdb=" OP1 DA M 4 " pdb=" OP2 DA M 4 " pdb=" O5' DA M 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.75 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" P DC K 4 " pdb=" OP1 DC K 4 " pdb=" OP2 DC K 4 " pdb=" O5' DC K 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.73 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" C3' DC L 67 " pdb=" C4' DC L 67 " pdb=" O3' DC L 67 " pdb=" C2' DC L 67 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.44e-01 ... (remaining 2863 not shown) Planarity restraints: 3731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 196 " -0.277 9.50e-02 1.11e+02 9.25e-02 9.42e+00 pdb=" NE ARG J 196 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG J 196 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG J 196 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 196 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG J 196 " 0.007 2.00e-02 2.50e+03 pdb="HH12 ARG J 196 " -0.006 2.00e-02 2.50e+03 pdb="HH21 ARG J 196 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG J 196 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 132 " -0.250 9.50e-02 1.11e+02 8.41e-02 9.11e+00 pdb=" NE ARG I 132 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG I 132 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG I 132 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG I 132 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG I 132 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG I 132 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG I 132 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG I 132 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU P 195 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" CD GLU P 195 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU P 195 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU P 195 " -0.014 2.00e-02 2.50e+03 ... (remaining 3728 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 8091 2.33 - 2.89: 64179 2.89 - 3.46: 79729 3.46 - 4.03: 121418 4.03 - 4.60: 170970 Nonbonded interactions: 444387 Sorted by model distance: nonbonded pdb=" HG SER A 18 " pdb=" H VAL A 27 " model vdw 1.757 2.100 nonbonded pdb=" HB3 LYS B 15 " pdb=" HZ2 LYS B 15 " model vdw 1.757 2.270 nonbonded pdb=" HB3 LYS I 217 " pdb=" HZ1 LYS I 217 " model vdw 1.771 2.270 nonbonded pdb=" OE1 GLU I 243 " pdb=" H GLU I 243 " model vdw 1.798 2.450 nonbonded pdb=" H TYR P 208 " pdb=" HD1 TYR P 208 " model vdw 1.813 2.100 ... (remaining 444382 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 'B' and resid 12 through 119) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 38 through 136) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 5.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 34.230 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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:8.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 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 : 0.006 0.039 18057 Z= 0.508 Angle : 0.779 10.574 25684 Z= 0.598 Chirality : 0.060 0.410 2866 Planarity : 0.006 0.120 2188 Dihedral : 24.973 165.626 7538 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.60 % Allowed : 14.56 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 2.07 (0.23), residues: 1338 helix: 2.57 (0.22), residues: 555 sheet: 0.61 (0.30), residues: 285 loop : 0.57 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG I 132 TYR 0.015 0.001 TYR I 73 PHE 0.008 0.001 PHE P 176 TRP 0.008 0.001 TRP I 201 HIS 0.005 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.51 (18055) covalent geometry : angle 0.77876 / 0.60 (25680) SS BOND : bond 0.00450 / 0.26 ( 2) SS BOND : angle 0.63138 / 0.35 ( 4) hydrogen bonds : bond 0.11082 / 7.84 ( 997) hydrogen bonds : angle 4.89819 / 3.59 ( 2503) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8953 (ttpp) cc_final: 0.8593 (tttp) REVERT: D 56 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8597 (tmtm) REVERT: E 38 LYS cc_start: 0.8605 (tppt) cc_final: 0.8321 (tmmt) REVERT: P 145 PHE cc_start: 0.7769 (m-80) cc_final: 0.7532 (m-80) outliers start: 7 outliers final: 6 residues processed: 201 average time/residue: 1.5318 time to fit residues: 335.8360 Evaluate side-chains 190 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain P residue 116 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN F 40 HIS I 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.081482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.058604 restraints weight = 78267.434| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.52 r_work: 0.2741 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.0572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18057 Z= 0.204 Angle : 0.652 9.525 25684 Z= 0.391 Chirality : 0.043 0.314 2866 Planarity : 0.005 0.057 2188 Dihedral : 28.209 168.737 4870 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.12 % Allowed : 13.87 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 2.13 (0.23), residues: 1338 helix: 2.52 (0.22), residues: 560 sheet: 1.02 (0.31), residues: 284 loop : 0.42 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 132 TYR 0.016 0.001 TYR I 73 PHE 0.007 0.001 PHE J 95 TRP 0.007 0.001 TRP I 190 HIS 0.006 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 (18055) covalent geometry : angle 0.65151 / 0.39 (25680) SS BOND : bond 0.00550 / 0.33 ( 2) SS BOND : angle 0.93577 / 0.50 ( 4) hydrogen bonds : bond 0.04769 / 3.27 ( 997) hydrogen bonds : angle 4.11743 / 2.98 ( 2503) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8203 (tttp) REVERT: B 118 LYS cc_start: 0.8364 (tptp) cc_final: 0.8163 (tmmt) REVERT: D 56 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8438 (tmtm) REVERT: E 121 MET cc_start: 0.8815 (mtm) cc_final: 0.8600 (mtt) REVERT: J 165 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8875 (mp) outliers start: 13 outliers final: 8 residues processed: 193 average time/residue: 1.5649 time to fit residues: 328.4398 Evaluate side-chains 192 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain P residue 109 CYS Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 143 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.081198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.058125 restraints weight = 78052.249| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.53 r_work: 0.2729 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18057 Z= 0.226 Angle : 0.636 8.556 25684 Z= 0.382 Chirality : 0.042 0.312 2866 Planarity : 0.005 0.051 2188 Dihedral : 28.375 169.022 4870 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.21 % Allowed : 13.01 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 2.11 (0.23), residues: 1338 helix: 2.52 (0.21), residues: 560 sheet: 1.09 (0.31), residues: 284 loop : 0.34 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 196 TYR 0.016 0.001 TYR I 73 PHE 0.007 0.001 PHE P 145 TRP 0.008 0.001 TRP I 190 HIS 0.006 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.23 (18055) covalent geometry : angle 0.63547 / 0.38 (25680) SS BOND : bond 0.00500 / 0.29 ( 2) SS BOND : angle 1.24892 / 0.66 ( 4) hydrogen bonds : bond 0.04774 / 3.27 ( 997) hydrogen bonds : angle 3.91278 / 2.83 ( 2503) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8194 (tttp) REVERT: B 118 LYS cc_start: 0.8393 (tptp) cc_final: 0.8187 (tmmt) REVERT: D 56 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8431 (tmtm) REVERT: E 121 MET cc_start: 0.8784 (mtm) cc_final: 0.8555 (mtt) REVERT: J 165 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8899 (mp) REVERT: P 140 ASP cc_start: 0.8676 (m-30) cc_final: 0.8368 (m-30) REVERT: P 190 ASP cc_start: 0.9073 (m-30) cc_final: 0.8835 (t0) outliers start: 14 outliers final: 9 residues processed: 193 average time/residue: 1.6027 time to fit residues: 336.8082 Evaluate side-chains 194 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain P residue 109 CYS Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 143 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 37 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.081555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.058609 restraints weight = 78023.650| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.52 r_work: 0.2745 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18057 Z= 0.183 Angle : 0.615 9.330 25684 Z= 0.370 Chirality : 0.041 0.310 2866 Planarity : 0.005 0.071 2188 Dihedral : 28.498 169.237 4870 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.29 % Allowed : 12.92 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 2.18 (0.23), residues: 1338 helix: 2.59 (0.22), residues: 560 sheet: 1.16 (0.31), residues: 284 loop : 0.34 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 196 TYR 0.016 0.001 TYR I 73 PHE 0.007 0.001 PHE F 68 TRP 0.006 0.001 TRP I 190 HIS 0.006 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (18055) covalent geometry : angle 0.61535 / 0.37 (25680) SS BOND : bond 0.00527 / 0.31 ( 2) SS BOND : angle 0.94605 / 0.49 ( 4) hydrogen bonds : bond 0.04184 / 2.86 ( 997) hydrogen bonds : angle 3.75449 / 2.71 ( 2503) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8192 (tttp) REVERT: B 118 LYS cc_start: 0.8396 (tptp) cc_final: 0.8186 (tmmt) REVERT: D 56 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8395 (tmtm) REVERT: E 38 LYS cc_start: 0.8888 (tppp) cc_final: 0.8387 (tmmt) REVERT: E 121 MET cc_start: 0.8746 (mtm) cc_final: 0.8524 (mtt) REVERT: J 42 ARG cc_start: 0.8811 (mtp-110) cc_final: 0.8519 (ptm160) REVERT: J 165 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8900 (mp) REVERT: P 140 ASP cc_start: 0.8713 (m-30) cc_final: 0.8421 (m-30) REVERT: P 186 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8017 (m110) REVERT: P 190 ASP cc_start: 0.9081 (m-30) cc_final: 0.8805 (t0) outliers start: 15 outliers final: 9 residues processed: 194 average time/residue: 1.5680 time to fit residues: 331.6042 Evaluate side-chains 194 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain P residue 109 CYS Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 186 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.081639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058748 restraints weight = 78268.654| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.52 r_work: 0.2742 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18057 Z= 0.188 Angle : 0.614 9.490 25684 Z= 0.368 Chirality : 0.041 0.309 2866 Planarity : 0.004 0.057 2188 Dihedral : 28.567 169.129 4870 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.12 % Allowed : 13.26 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 2.24 (0.23), residues: 1338 helix: 2.64 (0.22), residues: 560 sheet: 1.20 (0.32), residues: 284 loop : 0.37 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 85 TYR 0.016 0.001 TYR I 73 PHE 0.007 0.001 PHE P 126 TRP 0.005 0.001 TRP I 264 HIS 0.005 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.19 (18055) covalent geometry : angle 0.61397 / 0.37 (25680) SS BOND : bond 0.00456 / 0.28 ( 2) SS BOND : angle 1.04871 / 0.54 ( 4) hydrogen bonds : bond 0.04210 / 2.88 ( 997) hydrogen bonds : angle 3.65024 / 2.63 ( 2503) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8589 (ttpp) cc_final: 0.8191 (tttp) REVERT: B 118 LYS cc_start: 0.8404 (tptp) cc_final: 0.8194 (tmmt) REVERT: D 56 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8379 (tmtm) REVERT: E 38 LYS cc_start: 0.8850 (tppp) cc_final: 0.8338 (tmmt) REVERT: P 140 ASP cc_start: 0.8747 (m-30) cc_final: 0.8439 (m-30) REVERT: P 157 MET cc_start: 0.7903 (mpp) cc_final: 0.7648 (tpp) REVERT: P 190 ASP cc_start: 0.9116 (m-30) cc_final: 0.8798 (t0) outliers start: 13 outliers final: 10 residues processed: 191 average time/residue: 1.6320 time to fit residues: 339.4765 Evaluate side-chains 193 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain P residue 109 CYS Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 143 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 40 optimal weight: 0.0870 chunk 83 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.082231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.059285 restraints weight = 77885.812| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.53 r_work: 0.2760 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18057 Z= 0.155 Angle : 0.602 7.898 25684 Z= 0.361 Chirality : 0.041 0.301 2866 Planarity : 0.004 0.068 2188 Dihedral : 28.615 168.943 4870 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.38 % Allowed : 13.52 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 2.29 (0.23), residues: 1338 helix: 2.69 (0.22), residues: 560 sheet: 1.25 (0.32), residues: 284 loop : 0.35 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 196 TYR 0.015 0.001 TYR I 73 PHE 0.007 0.001 PHE F 68 TRP 0.005 0.001 TRP I 190 HIS 0.005 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (18055) covalent geometry : angle 0.60196 / 0.36 (25680) SS BOND : bond 0.00438 / 0.26 ( 2) SS BOND : angle 0.82897 / 0.43 ( 4) hydrogen bonds : bond 0.03838 / 2.63 ( 997) hydrogen bonds : angle 3.57943 / 2.58 ( 2503) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8575 (ttpp) cc_final: 0.8194 (tttp) REVERT: B 118 LYS cc_start: 0.8425 (tptp) cc_final: 0.8185 (tmmt) REVERT: D 56 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8360 (tmtm) REVERT: E 38 LYS cc_start: 0.8839 (tppp) cc_final: 0.8328 (tmmt) REVERT: P 140 ASP cc_start: 0.8757 (m-30) cc_final: 0.8482 (m-30) REVERT: P 157 MET cc_start: 0.7888 (mpp) cc_final: 0.7652 (tpp) REVERT: P 186 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.7968 (m110) REVERT: P 190 ASP cc_start: 0.9105 (m-30) cc_final: 0.8749 (t0) outliers start: 16 outliers final: 11 residues processed: 194 average time/residue: 1.4591 time to fit residues: 308.5258 Evaluate side-chains 195 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 176 CYS Chi-restraints excluded: chain P residue 109 CYS Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 143 ARG Chi-restraints excluded: chain P residue 186 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 121 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.081461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.058500 restraints weight = 77932.736| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.52 r_work: 0.2740 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18057 Z= 0.204 Angle : 0.621 8.733 25684 Z= 0.369 Chirality : 0.041 0.307 2866 Planarity : 0.005 0.068 2188 Dihedral : 28.632 168.887 4870 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.29 % Allowed : 13.70 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 2.26 (0.23), residues: 1338 helix: 2.67 (0.22), residues: 562 sheet: 1.20 (0.32), residues: 285 loop : 0.35 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 196 TYR 0.016 0.001 TYR I 73 PHE 0.009 0.001 PHE P 126 TRP 0.005 0.001 TRP I 264 HIS 0.005 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 (18055) covalent geometry : angle 0.62089 / 0.37 (25680) SS BOND : bond 0.00493 / 0.30 ( 2) SS BOND : angle 1.31790 / 0.66 ( 4) hydrogen bonds : bond 0.04307 / 2.94 ( 997) hydrogen bonds : angle 3.55600 / 2.56 ( 2503) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8181 (tttp) REVERT: B 118 LYS cc_start: 0.8436 (tptp) cc_final: 0.8197 (tmmt) REVERT: D 56 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8374 (tmtm) REVERT: I 227 ASP cc_start: 0.8527 (t0) cc_final: 0.8312 (t0) REVERT: P 140 ASP cc_start: 0.8776 (m-30) cc_final: 0.8508 (m-30) REVERT: P 157 MET cc_start: 0.7910 (mpp) cc_final: 0.7690 (tpp) REVERT: P 190 ASP cc_start: 0.9115 (m-30) cc_final: 0.8759 (t0) outliers start: 15 outliers final: 11 residues processed: 195 average time/residue: 1.5231 time to fit residues: 324.2657 Evaluate side-chains 195 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 176 CYS Chi-restraints excluded: chain P residue 109 CYS Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 143 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.081090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.058176 restraints weight = 78149.948| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.52 r_work: 0.2729 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18057 Z= 0.231 Angle : 0.636 9.629 25684 Z= 0.374 Chirality : 0.042 0.308 2866 Planarity : 0.005 0.070 2188 Dihedral : 28.673 169.271 4870 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.38 % Allowed : 13.78 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 2.21 (0.23), residues: 1338 helix: 2.65 (0.22), residues: 562 sheet: 1.19 (0.32), residues: 285 loop : 0.29 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 196 TYR 0.016 0.001 TYR I 73 PHE 0.008 0.001 PHE P 126 TRP 0.006 0.001 TRP I 264 HIS 0.005 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.23 (18055) covalent geometry : angle 0.63553 / 0.37 (25680) SS BOND : bond 0.00538 / 0.32 ( 2) SS BOND : angle 1.47768 / 0.76 ( 4) hydrogen bonds : bond 0.04463 / 3.04 ( 997) hydrogen bonds : angle 3.55341 / 2.56 ( 2503) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8196 (tttp) REVERT: B 118 LYS cc_start: 0.8459 (tptp) cc_final: 0.8225 (tmmt) REVERT: D 56 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8400 (tmtm) REVERT: E 121 MET cc_start: 0.8767 (mtp) cc_final: 0.8526 (mtt) REVERT: I 227 ASP cc_start: 0.8527 (t0) cc_final: 0.8312 (t0) REVERT: P 140 ASP cc_start: 0.8823 (m-30) cc_final: 0.8543 (m-30) REVERT: P 157 MET cc_start: 0.7913 (mpp) cc_final: 0.7702 (tpp) REVERT: P 190 ASP cc_start: 0.9158 (m-30) cc_final: 0.8793 (t0) outliers start: 16 outliers final: 10 residues processed: 193 average time/residue: 1.4787 time to fit residues: 311.4115 Evaluate side-chains 195 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 143 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 122 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.082058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.059129 restraints weight = 77882.538| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.52 r_work: 0.2753 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18057 Z= 0.150 Angle : 0.616 10.959 25684 Z= 0.365 Chirality : 0.041 0.298 2866 Planarity : 0.004 0.074 2188 Dihedral : 28.706 169.068 4870 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.03 % Allowed : 14.21 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 2.27 (0.23), residues: 1338 helix: 2.70 (0.22), residues: 562 sheet: 1.20 (0.32), residues: 285 loop : 0.33 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 196 TYR 0.016 0.001 TYR I 73 PHE 0.011 0.001 PHE P 126 TRP 0.007 0.001 TRP I 190 HIS 0.005 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (18055) covalent geometry : angle 0.61589 / 0.37 (25680) SS BOND : bond 0.00402 / 0.24 ( 2) SS BOND : angle 0.87216 / 0.44 ( 4) hydrogen bonds : bond 0.03844 / 2.63 ( 997) hydrogen bonds : angle 3.51548 / 2.53 ( 2503) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8557 (ttpp) cc_final: 0.8174 (tttp) REVERT: B 118 LYS cc_start: 0.8469 (tptp) cc_final: 0.8237 (tmmt) REVERT: D 56 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8370 (tmtm) REVERT: E 121 MET cc_start: 0.8732 (mtp) cc_final: 0.8500 (mtt) REVERT: I 227 ASP cc_start: 0.8539 (t0) cc_final: 0.8316 (t0) REVERT: P 140 ASP cc_start: 0.8819 (m-30) cc_final: 0.8547 (m-30) REVERT: P 157 MET cc_start: 0.7876 (mpp) cc_final: 0.7632 (tpp) REVERT: P 190 ASP cc_start: 0.9155 (m-30) cc_final: 0.8779 (t0) outliers start: 12 outliers final: 10 residues processed: 196 average time/residue: 1.4625 time to fit residues: 312.1357 Evaluate side-chains 197 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 143 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 41 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.081689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058718 restraints weight = 77919.938| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.52 r_work: 0.2743 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18057 Z= 0.191 Angle : 0.632 9.887 25684 Z= 0.370 Chirality : 0.041 0.304 2866 Planarity : 0.005 0.080 2188 Dihedral : 28.716 168.866 4870 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.21 % Allowed : 14.21 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 2.30 (0.23), residues: 1338 helix: 2.73 (0.22), residues: 562 sheet: 1.24 (0.32), residues: 285 loop : 0.34 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 196 TYR 0.015 0.001 TYR I 73 PHE 0.009 0.001 PHE P 126 TRP 0.005 0.001 TRP I 264 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 (18055) covalent geometry : angle 0.63163 / 0.37 (25680) SS BOND : bond 0.00459 / 0.28 ( 2) SS BOND : angle 1.21832 / 0.64 ( 4) hydrogen bonds : bond 0.04107 / 2.80 ( 997) hydrogen bonds : angle 3.48598 / 2.51 ( 2503) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8169 (tttp) REVERT: B 118 LYS cc_start: 0.8492 (tptp) cc_final: 0.8251 (tmmt) REVERT: C 56 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8909 (mmtm) REVERT: D 56 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8368 (tmtm) REVERT: E 121 MET cc_start: 0.8734 (mtp) cc_final: 0.8513 (mtt) REVERT: I 227 ASP cc_start: 0.8513 (t0) cc_final: 0.8289 (t0) REVERT: P 140 ASP cc_start: 0.8826 (m-30) cc_final: 0.8546 (m-30) REVERT: P 190 ASP cc_start: 0.9160 (m-30) cc_final: 0.8806 (t0) outliers start: 14 outliers final: 11 residues processed: 194 average time/residue: 1.5918 time to fit residues: 336.2057 Evaluate side-chains 199 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 143 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 27 optimal weight: 0.1980 chunk 85 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.081623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.058675 restraints weight = 78302.429| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.52 r_work: 0.2745 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18057 Z= 0.187 Angle : 0.625 11.169 25684 Z= 0.368 Chirality : 0.041 0.300 2866 Planarity : 0.005 0.078 2188 Dihedral : 28.740 168.809 4870 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.03 % Allowed : 14.30 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 2.31 (0.23), residues: 1338 helix: 2.72 (0.22), residues: 562 sheet: 1.23 (0.32), residues: 285 loop : 0.34 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 42 TYR 0.016 0.001 TYR I 73 PHE 0.015 0.001 PHE P 126 TRP 0.005 0.001 TRP J 190 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (18055) covalent geometry : angle 0.62538 / 0.37 (25680) SS BOND : bond 0.00443 / 0.27 ( 2) SS BOND : angle 1.17631 / 0.61 ( 4) hydrogen bonds : bond 0.04046 / 2.76 ( 997) hydrogen bonds : angle 3.47175 / 2.50 ( 2503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15609.26 seconds wall clock time: 263 minutes 41.20 seconds (15821.20 seconds total)