Starting phenix.real_space_refine on Mon Jul 6 02:36:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zqb_74563/07_2026/9zqb_74563.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zqb_74563/07_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_74563/07_2026/9zqb_74563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zqb_74563/07_2026/9zqb_74563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zqb_74563/07_2026/9zqb_74563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zqb_74563/07_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-dev-6108/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: 5.42, per 1000 atoms: 0.17 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: 3.09 Conformation dependent library (CDL) restraints added in 709.5 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: 5.19 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: 7.12 Time building geometry restraints manager: 4.18 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: 57776 2.11 - 4.23: 1129 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: 4.530 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: 0.210 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.930 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.510 ------------------------------------------------------------------------------- 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= 0.507 Angle : 0.774 10.574 25684 Z= 0.593 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 0.77388 / 0.59 (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 : 0.718 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: 0.8953 (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: 1.5780 time to fit residues: 345.4043 Evaluate side-chains 191 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 184 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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: 6.9990 chunk 124 optimal weight: 5.9990 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 = 0.3476 r_free = 0.3476 target = 0.081340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058356 restraints weight = 78168.749| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.54 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: 0.8750 moved from start: 0.0561 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= 0.206 Angle : 0.645 9.464 25684 Z= 0.389 Chirality : 0.042 0.304 2866 Planarity : 0.005 0.055 2188 Dihedral : 28.235 169.174 4870 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.12 % Allowed : 13.70 % Favored : 85.19 % 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: 2.53 (0.22), residues: 560 sheet: 1.01 (0.31), residues: 284 loop : 0.43 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 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 0.00397 / 0.21 (18055) covalent geometry : angle 0.64541 / 0.39 (25680) SS BOND : bond 0.00573 / 0.34 ( 2) SS BOND : angle 0.98476 / 0.53 ( 4) hydrogen bonds : bond 0.04775 / 3.28 ( 997) hydrogen bonds : angle 4.12208 / 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 : 0.716 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: 0.8610 (ttpp) cc_final: 0.8203 (tttp) REVERT: B 118 LYS cc_start: 0.8363 (tptp) cc_final: 0.8162 (tmmt) REVERT: C 85 ARG cc_start: 0.8919 (mmt90) cc_final: 0.8683 (mmt90) REVERT: D 56 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8438 (tmtm) REVERT: D 104 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8649 (mm-30) REVERT: E 121 MET cc_start: 0.8826 (mtm) cc_final: 0.8613 (mtt) REVERT: J 165 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8873 (mp) outliers start: 13 outliers final: 8 residues processed: 193 average time/residue: 1.6403 time to fit residues: 343.4904 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 D residue 104 GLU 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: 2.9990 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: 5.9990 chunk 71 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.080625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.057562 restraints weight = 78063.749| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.56 r_work: 0.2717 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18057 Z= 0.266 Angle : 0.645 8.243 25684 Z= 0.386 Chirality : 0.043 0.305 2866 Planarity : 0.005 0.054 2188 Dihedral : 28.420 170.183 4870 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.29 % Allowed : 12.75 % Favored : 85.96 % 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: 2.05 (0.23), residues: 1338 helix: 2.49 (0.21), residues: 560 sheet: 1.06 (0.31), residues: 284 loop : 0.29 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 196 TYR 0.017 0.002 TYR I 73 PHE 0.017 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 0.00529 / 0.27 (18055) covalent geometry : angle 0.64475 / 0.39 (25680) SS BOND : bond 0.00603 / 0.36 ( 2) SS BOND : angle 1.45249 / 0.76 ( 4) hydrogen bonds : bond 0.05131 / 3.50 ( 997) hydrogen bonds : angle 3.91527 / 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 201 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.653 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: 0.8625 (ttpp) cc_final: 0.8210 (tttp) REVERT: B 118 LYS cc_start: 0.8388 (tptp) cc_final: 0.8182 (tmmt) REVERT: D 56 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8429 (tmtm) REVERT: J 165 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8899 (mp) REVERT: P 140 ASP cc_start: 0.8690 (m-30) cc_final: 0.8384 (m-30) REVERT: P 190 ASP cc_start: 0.9065 (m-30) cc_final: 0.8830 (t0) outliers start: 15 outliers final: 9 residues processed: 193 average time/residue: 1.6615 time to fit residues: 347.5663 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 : 0.732 ------------------------------------------------------------------------------- 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: 0.5980 chunk 157 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 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: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.082048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.059068 restraints weight = 77944.235| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.53 r_work: 0.2755 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 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 0.025 18057 Z= 0.153 Angle : 0.600 9.670 25684 Z= 0.366 Chirality : 0.041 0.292 2866 Planarity : 0.004 0.063 2188 Dihedral : 28.556 170.473 4870 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.38 % Allowed : 12.75 % Favored : 85.87 % 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: 2.17 (0.23), residues: 1338 helix: 2.59 (0.22), residues: 560 sheet: 1.15 (0.31), residues: 284 loop : 0.32 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 85 TYR 0.015 0.001 TYR I 73 PHE 0.006 0.001 PHE F 68 TRP 0.006 0.001 TRP I 190 HIS 0.005 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (18055) covalent geometry : angle 0.59994 / 0.37 (25680) SS BOND : bond 0.00433 / 0.26 ( 2) SS BOND : angle 0.79632 / 0.44 ( 4) hydrogen bonds : bond 0.03948 / 2.71 ( 997) hydrogen bonds : angle 3.75625 / 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 205 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.759 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: 0.8586 (ttpp) cc_final: 0.8181 (tttp) REVERT: B 118 LYS cc_start: 0.8382 (tptp) cc_final: 0.8178 (tmmt) REVERT: D 56 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8385 (tmtm) REVERT: E 38 LYS cc_start: 0.8849 (tppp) cc_final: 0.8362 (tmmt) REVERT: I 227 ASP cc_start: 0.8594 (t70) cc_final: 0.8358 (t0) REVERT: J 165 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8891 (mp) REVERT: P 140 ASP cc_start: 0.8662 (m-30) cc_final: 0.8360 (m-30) REVERT: P 186 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8095 (m110) REVERT: P 190 ASP cc_start: 0.9074 (m-30) cc_final: 0.8800 (t0) outliers start: 16 outliers final: 9 residues processed: 198 average time/residue: 1.6665 time to fit residues: 358.7377 Evaluate side-chains 198 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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: 0.9990 chunk 114 optimal weight: 4.9990 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: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.082106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.059176 restraints weight = 78063.843| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.52 r_work: 0.2759 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.0928 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= 0.163 Angle : 0.597 9.530 25684 Z= 0.362 Chirality : 0.040 0.294 2866 Planarity : 0.004 0.056 2188 Dihedral : 28.590 170.240 4870 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.12 % Allowed : 13.09 % 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: 2.25 (0.23), residues: 1338 helix: 2.63 (0.22), residues: 566 sheet: 1.20 (0.32), residues: 284 loop : 0.37 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 196 TYR 0.016 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 0.00300 / 0.16 (18055) covalent geometry : angle 0.59700 / 0.36 (25680) SS BOND : bond 0.00427 / 0.25 ( 2) SS BOND : angle 0.96184 / 0.51 ( 4) hydrogen bonds : bond 0.03938 / 2.70 ( 997) hydrogen bonds : angle 3.64909 / 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 202 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8589 (ttpp) cc_final: 0.8193 (tttp) REVERT: B 118 LYS cc_start: 0.8395 (tptp) cc_final: 0.8186 (tmmt) REVERT: D 56 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8364 (tmtm) REVERT: E 38 LYS cc_start: 0.8850 (tppp) cc_final: 0.8335 (tmmt) REVERT: I 227 ASP cc_start: 0.8585 (t70) cc_final: 0.8348 (t0) REVERT: P 140 ASP cc_start: 0.8743 (m-30) cc_final: 0.8431 (m-30) REVERT: P 157 MET cc_start: 0.7860 (mpp) cc_final: 0.7606 (tpp) REVERT: P 190 ASP cc_start: 0.9104 (m-30) cc_final: 0.8797 (t0) outliers start: 13 outliers final: 10 residues processed: 195 average time/residue: 1.5846 time to fit residues: 335.7789 Evaluate side-chains 196 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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: 2.9990 chunk 83 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.080727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.057665 restraints weight = 77817.982| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.55 r_work: 0.2719 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18057 Z= 0.252 Angle : 0.638 9.589 25684 Z= 0.378 Chirality : 0.042 0.304 2866 Planarity : 0.005 0.088 2188 Dihedral : 28.634 170.767 4870 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.46 % Allowed : 13.01 % Favored : 85.53 % 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: 2.17 (0.23), residues: 1338 helix: 2.59 (0.21), residues: 562 sheet: 1.19 (0.32), residues: 284 loop : 0.28 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 196 TYR 0.017 0.002 TYR I 73 PHE 0.008 0.001 PHE F 68 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 0.00503 / 0.25 (18055) covalent geometry : angle 0.63774 / 0.38 (25680) SS BOND : bond 0.00582 / 0.35 ( 2) SS BOND : angle 1.59855 / 0.81 ( 4) hydrogen bonds : bond 0.04843 / 3.30 ( 997) hydrogen bonds : angle 3.63380 / 2.62 ( 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 204 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8197 (tttp) REVERT: B 118 LYS cc_start: 0.8425 (tptp) cc_final: 0.8210 (tmmt) REVERT: D 56 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8399 (tmtm) REVERT: I 227 ASP cc_start: 0.8585 (t70) cc_final: 0.8334 (t0) REVERT: P 140 ASP cc_start: 0.8825 (m-30) cc_final: 0.8548 (m-30) REVERT: P 157 MET cc_start: 0.7934 (mpp) cc_final: 0.7701 (tpp) REVERT: P 190 ASP cc_start: 0.9123 (m-30) cc_final: 0.8765 (t0) outliers start: 17 outliers final: 9 residues processed: 196 average time/residue: 1.4816 time to fit residues: 316.3897 Evaluate side-chains 193 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 143 ARG 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: 1.9990 chunk 15 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.081689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.058801 restraints weight = 77840.246| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.52 r_work: 0.2747 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18057 Z= 0.166 Angle : 0.606 8.944 25684 Z= 0.364 Chirality : 0.041 0.291 2866 Planarity : 0.004 0.065 2188 Dihedral : 28.704 170.958 4868 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.21 % Allowed : 13.44 % Favored : 85.36 % 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: 2.23 (0.23), residues: 1338 helix: 2.65 (0.22), residues: 562 sheet: 1.21 (0.32), residues: 284 loop : 0.31 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 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 190 HIS 0.005 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (18055) covalent geometry : angle 0.60569 / 0.36 (25680) SS BOND : bond 0.00453 / 0.27 ( 2) SS BOND : angle 0.98091 / 0.50 ( 4) hydrogen bonds : bond 0.04005 / 2.74 ( 997) hydrogen bonds : angle 3.57349 / 2.57 ( 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: 14 poor density : 186 time to evaluate : 0.734 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: 0.8581 (ttpp) cc_final: 0.8193 (tttp) REVERT: A 73 ASN cc_start: 0.8847 (t0) cc_final: 0.8425 (t160) REVERT: B 118 LYS cc_start: 0.8418 (tptp) cc_final: 0.8191 (tmmt) REVERT: D 56 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8363 (tmtm) REVERT: E 38 LYS cc_start: 0.8787 (tppp) cc_final: 0.8326 (tmmt) REVERT: I 227 ASP cc_start: 0.8574 (t70) cc_final: 0.8316 (t0) REVERT: P 140 ASP cc_start: 0.8746 (m-30) cc_final: 0.8477 (m-30) REVERT: P 157 MET cc_start: 0.7887 (mpp) cc_final: 0.7667 (tpp) REVERT: P 190 ASP cc_start: 0.9112 (m-30) cc_final: 0.8761 (t0) outliers start: 14 outliers final: 9 residues processed: 193 average time/residue: 1.6771 time to fit residues: 351.3622 Evaluate side-chains 195 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 39 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 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 = 0.3469 r_free = 0.3469 target = 0.080997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.057940 restraints weight = 77994.750| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.55 r_work: 0.2723 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18057 Z= 0.238 Angle : 0.637 9.963 25684 Z= 0.376 Chirality : 0.042 0.302 2866 Planarity : 0.005 0.079 2188 Dihedral : 28.727 171.298 4868 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.29 % Allowed : 13.87 % 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: 2.18 (0.23), residues: 1338 helix: 2.62 (0.21), residues: 562 sheet: 1.18 (0.32), residues: 285 loop : 0.26 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 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 0.00474 / 0.24 (18055) covalent geometry : angle 0.63666 / 0.38 (25680) SS BOND : bond 0.00607 / 0.36 ( 2) SS BOND : angle 1.49707 / 0.77 ( 4) hydrogen bonds : bond 0.04584 / 3.12 ( 997) hydrogen bonds : angle 3.57034 / 2.57 ( 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: 15 poor density : 187 time to evaluate : 0.738 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: 0.8583 (ttpp) cc_final: 0.8196 (tttp) REVERT: A 73 ASN cc_start: 0.8880 (t0) cc_final: 0.8468 (t160) REVERT: B 118 LYS cc_start: 0.8471 (tptp) cc_final: 0.8239 (tmmt) REVERT: D 56 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8396 (tmtm) REVERT: E 38 LYS cc_start: 0.8827 (tppp) cc_final: 0.8376 (tmmt) REVERT: E 121 MET cc_start: 0.8757 (mtp) cc_final: 0.8527 (mtt) REVERT: I 227 ASP cc_start: 0.8563 (t70) cc_final: 0.8286 (t0) REVERT: P 140 ASP cc_start: 0.8824 (m-30) cc_final: 0.8552 (m-30) REVERT: P 157 MET cc_start: 0.7926 (mpp) cc_final: 0.7722 (tpp) REVERT: P 190 ASP cc_start: 0.9143 (m-30) cc_final: 0.8778 (t0) outliers start: 15 outliers final: 10 residues processed: 193 average time/residue: 1.5994 time to fit residues: 335.7625 Evaluate side-chains 196 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 H residue 26 ASP Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain J residue 165 LEU 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: 0.7980 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.081568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.058574 restraints weight = 78054.639| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.54 r_work: 0.2740 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1156 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= 0.181 Angle : 0.619 10.674 25684 Z= 0.368 Chirality : 0.041 0.292 2866 Planarity : 0.005 0.075 2188 Dihedral : 28.770 171.337 4868 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.95 % Allowed : 14.21 % 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: 1.20 (0.32), residues: 285 loop : 0.28 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 196 TYR 0.016 0.001 TYR I 73 PHE 0.011 0.001 PHE P 126 TRP 0.006 0.001 TRP I 190 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (18055) covalent geometry : angle 0.61898 / 0.37 (25680) SS BOND : bond 0.00456 / 0.28 ( 2) SS BOND : angle 1.08874 / 0.57 ( 4) hydrogen bonds : bond 0.04099 / 2.80 ( 997) hydrogen bonds : angle 3.53991 / 2.55 ( 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 200 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8184 (tttp) REVERT: A 73 ASN cc_start: 0.8878 (t0) cc_final: 0.8466 (t160) REVERT: B 118 LYS cc_start: 0.8471 (tptp) cc_final: 0.8240 (tmmt) REVERT: D 56 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8391 (tmtm) REVERT: E 38 LYS cc_start: 0.8821 (tppp) cc_final: 0.8382 (tmmt) REVERT: E 121 MET cc_start: 0.8737 (mtp) cc_final: 0.8519 (mtt) REVERT: I 227 ASP cc_start: 0.8558 (t70) cc_final: 0.8277 (t0) REVERT: P 140 ASP cc_start: 0.8818 (m-30) cc_final: 0.8538 (m-30) REVERT: P 157 MET cc_start: 0.7904 (mpp) cc_final: 0.7658 (tpp) REVERT: P 190 ASP cc_start: 0.9156 (m-30) cc_final: 0.8785 (t0) outliers start: 11 outliers final: 9 residues processed: 194 average time/residue: 1.5237 time to fit residues: 321.6626 Evaluate side-chains 197 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 165 LEU 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: 1.9990 chunk 151 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.081593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058652 restraints weight = 77938.024| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.52 r_work: 0.2741 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1193 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= 0.185 Angle : 0.621 9.548 25684 Z= 0.368 Chirality : 0.041 0.294 2866 Planarity : 0.005 0.083 2188 Dihedral : 28.792 171.307 4868 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.03 % Allowed : 14.13 % 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: 2.25 (0.23), residues: 1338 helix: 2.68 (0.22), residues: 562 sheet: 1.21 (0.32), residues: 285 loop : 0.30 (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 0.009 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 0.00359 / 0.19 (18055) covalent geometry : angle 0.62069 / 0.37 (25680) SS BOND : bond 0.00481 / 0.29 ( 2) SS BOND : angle 1.14711 / 0.61 ( 4) hydrogen bonds : bond 0.04053 / 2.77 ( 997) hydrogen bonds : angle 3.50730 / 2.52 ( 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 203 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8170 (tttp) REVERT: A 73 ASN cc_start: 0.8888 (t0) cc_final: 0.8460 (t160) REVERT: B 118 LYS cc_start: 0.8493 (tptp) cc_final: 0.8251 (tmmt) REVERT: D 56 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8370 (tmtm) REVERT: E 38 LYS cc_start: 0.8835 (tppp) cc_final: 0.8399 (tmmt) REVERT: E 121 MET cc_start: 0.8731 (mtp) cc_final: 0.8517 (mtt) REVERT: I 227 ASP cc_start: 0.8547 (t70) cc_final: 0.8256 (t0) REVERT: P 140 ASP cc_start: 0.8848 (m-30) cc_final: 0.8568 (m-30) REVERT: P 190 ASP cc_start: 0.9158 (m-30) cc_final: 0.8790 (t0) outliers start: 12 outliers final: 8 residues processed: 196 average time/residue: 1.6094 time to fit residues: 344.9519 Evaluate side-chains 197 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 143 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.081434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.058603 restraints weight = 78445.996| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.52 r_work: 0.2737 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18057 Z= 0.199 Angle : 0.623 11.065 25684 Z= 0.369 Chirality : 0.041 0.295 2866 Planarity : 0.005 0.078 2188 Dihedral : 28.811 171.242 4868 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.86 % Allowed : 14.21 % Favored : 84.93 % 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: 2.69 (0.22), residues: 562 sheet: 1.23 (0.32), residues: 285 loop : 0.30 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 196 TYR 0.016 0.001 TYR I 73 PHE 0.017 0.001 PHE P 126 TRP 0.006 0.001 TRP I 190 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 (18055) covalent geometry : angle 0.62309 / 0.37 (25680) SS BOND : bond 0.00489 / 0.30 ( 2) SS BOND : angle 1.27179 / 0.67 ( 4) hydrogen bonds : bond 0.04164 / 2.84 ( 997) hydrogen bonds : angle 3.49470 / 2.51 ( 2503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16076.84 seconds wall clock time: 271 minutes 27.33 seconds (16287.33 seconds total)