Starting phenix.real_space_refine on Sun Aug 9 04:09:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zq9_74561/08_2026/9zq9_74561.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zq9_74561/08_2026/9zq9_74561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zq9_74561/08_2026/9zq9_74561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zq9_74561/08_2026/9zq9_74561.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zq9_74561/08_2026/9zq9_74561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zq9_74561/08_2026/9zq9_74561.map" } resolution = 3.3 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= 0.002 sd= 0.013 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 9854 2.51 5 N 3145 2.21 5 O 3854 1.98 5 H 14628 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 31827 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: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1722 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "D" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1627 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} 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: "P" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1972 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} 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: "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: "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: "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 Time building chain proxies: 4.87, per 1000 atoms: 0.15 Number of scatterers: 31827 At special positions: 0 Unit cell: (145.6, 151.97, 133.77, 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 3854 8.00 N 3145 7.00 C 9854 6.00 H 14628 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS J 47 " - pdb=" SG CYS J 112 " distance=2.04 Simple disulfide: pdb=" SG CYS I 47 " - pdb=" SG CYS I 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: 2.78 Conformation dependent library (CDL) restraints added in 676.1 milliseconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2570 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 26 sheets defined 44.5% alpha, 23.3% beta 153 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 27 through 36 Processing helix chain 'A' and resid 46 through 73 Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.556A pdb=" N LEU A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) 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 removed outlier: 3.855A pdb=" N ILE B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 73 Processing helix chain 'B' and resid 79 through 89 removed outlier: 3.657A pdb=" N LEU B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) 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 46 Processing helix chain 'C' and resid 54 through 83 removed outlier: 3.768A pdb=" N ASN C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 101 Processing helix chain 'C' and resid 103 through 123 removed outlier: 4.032A pdb=" N LYS C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 removed outlier: 3.676A pdb=" N GLN D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 47 " --> pdb=" O VAL D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 83 removed outlier: 3.834A pdb=" N ASN D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 103 through 124 removed outlier: 4.166A pdb=" N LYS D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER D 123 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.570A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 115 removed outlier: 3.552A pdb=" N ASP E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.671A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 64 through 78 removed outlier: 3.568A pdb=" N PHE F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 115 removed outlier: 3.764A pdb=" N VAL F 90 " --> pdb=" O GLN F 86 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET F 91 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA F 115 " --> pdb=" O SER F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 132 removed outlier: 3.697A pdb=" N ILE F 125 " --> pdb=" O MET F 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 31 Processing helix chain 'G' and resid 32 through 44 Processing helix chain 'G' and resid 51 through 78 removed outlier: 4.013A pdb=" N GLU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP G 70 " --> pdb=" O ASN G 66 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 95 removed outlier: 3.516A pdb=" N VAL G 88 " --> pdb=" O THR G 84 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN G 95 " --> pdb=" O ALA G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 31 Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 51 through 78 removed outlier: 3.952A pdb=" N GLU H 55 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA H 78 " --> pdb=" O TYR H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 95 removed outlier: 3.607A pdb=" N GLN H 95 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 102 Processing helix chain 'P' and resid 168 through 185 removed outlier: 3.560A pdb=" N ALA P 172 " --> pdb=" O ASN P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 194 removed outlier: 4.905A pdb=" N GLU P 192 " --> pdb=" O GLU P 189 " (cutoff:3.500A) 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 216 through 219 Processing helix chain 'J' and resid 228 through 231 Processing helix chain 'J' and resid 241 through 245 Processing helix chain 'I' and resid 103 through 107 removed outlier: 4.045A pdb=" N THR I 107 " --> pdb=" O SER I 104 " (cutoff:3.500A) 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 sheet with id=AA1, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.869A pdb=" N THR A 101 " --> pdb=" O TYR G 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 removed outlier: 7.919A pdb=" N ARG B 42 " --> pdb=" O ILE D 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 102 removed outlier: 6.736A pdb=" N THR B 101 " --> pdb=" O TYR H 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.145A pdb=" N ARG E 84 " --> pdb=" O VAL G 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA8, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.672A pdb=" N ARG F 84 " --> pdb=" O VAL H 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 119 through 120 Processing sheet with id=AB1, first strand: chain 'P' and resid 105 through 107 Processing sheet with id=AB2, first strand: chain 'P' and resid 105 through 107 removed outlier: 4.301A pdb=" N MET P 118 " --> pdb=" O LEU P 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 109 through 110 Processing sheet with id=AB4, first strand: chain 'J' and resid 29 through 31 removed outlier: 3.504A pdb=" N VAL J 43 " --> pdb=" O ILE J 99 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE J 95 " --> pdb=" O CYS J 47 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP J 94 " --> pdb=" O SER J 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 34 through 38 removed outlier: 3.620A pdb=" N ALA J 108 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU J 57 " --> pdb=" O TYR J 73 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR J 73 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP J 59 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 34 through 38 removed outlier: 3.620A pdb=" N ALA J 108 " --> pdb=" O LEU J 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 157 through 159 Processing sheet with id=AB8, first strand: chain 'J' and resid 172 through 174 Processing sheet with id=AB9, first strand: chain 'J' and resid 212 through 214 removed outlier: 6.852A pdb=" N TRP J 190 " --> pdb=" O ILE J 202 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR J 204 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE J 188 " --> pdb=" O TYR J 204 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS J 253 " --> pdb=" O THR J 187 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA J 251 " --> pdb=" O GLN J 189 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR J 263 " --> pdb=" O ARG J 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 212 through 214 removed outlier: 6.852A pdb=" N TRP J 190 " --> pdb=" O ILE J 202 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR J 204 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE J 188 " --> pdb=" O TYR J 204 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS J 253 " --> pdb=" O THR J 187 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA J 251 " --> pdb=" O GLN J 189 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 28 through 31 removed outlier: 6.405A pdb=" N GLN I 93 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N GLN I 51 " --> pdb=" O SER I 91 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N SER I 91 " --> pdb=" O GLN I 51 " (cutoff:3.500A) removed outlier: 12.446A pdb=" N ILE I 53 " --> pdb=" O SER I 89 " (cutoff:3.500A) removed outlier: 12.450A pdb=" N SER I 89 " --> pdb=" O ILE I 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.342A pdb=" N MET I 35 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LYS I 131 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA I 37 " --> pdb=" O LYS I 131 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA I 108 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP I 59 " --> pdb=" O LEU I 71 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.342A pdb=" N MET I 35 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LYS I 131 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA I 37 " --> pdb=" O LYS I 131 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA I 108 " --> pdb=" O LEU I 128 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 157 through 160 Processing sheet with id=AC6, first strand: chain 'I' and resid 164 through 166 removed outlier: 3.540A pdb=" N LYS I 253 " --> pdb=" O THR I 187 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE I 188 " --> pdb=" O TYR I 204 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR I 204 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP I 190 " --> pdb=" O ILE I 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 164 through 166 removed outlier: 4.251A pdb=" N TYR I 263 " --> pdb=" O ARG I 252 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 171 through 174 587 hydrogen bonds defined for protein. 1599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 392 hydrogen bonds 784 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 7.62 Time building geometry restraints manager: 3.90 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: 14621 1.03 - 1.23: 222 1.23 - 1.42: 8175 1.42 - 1.62: 9689 1.62 - 1.82: 69 Bond restraints: 32776 Sorted by residual: bond pdb=" C1' DC M 29 " pdb=" N1 DC M 29 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.33e+00 bond pdb=" C1' DC L 100 " pdb=" N1 DC L 100 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.14e+00 bond pdb=" C3' DC L 51 " pdb=" C2' DC L 51 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.25e+00 bond pdb=" C3' DT L 106 " pdb=" C2' DT L 106 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.06e+00 bond pdb=" C3' DA M 47 " pdb=" C2' DA M 47 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.62e+00 ... (remaining 32771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 58415 2.15 - 4.29: 881 4.29 - 6.44: 6 6.44 - 8.58: 0 8.58 - 10.73: 4 Bond angle restraints: 59306 Sorted by residual: angle pdb=" O4' DA M 124 " pdb=" C4' DA M 124 " pdb=" C3' DA M 124 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT L 71 " pdb=" C4 DT L 71 " pdb=" O4 DT L 71 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT L 31 " pdb=" C4 DT L 31 " pdb=" O4 DT L 31 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT M 99 " pdb=" C4 DT M 99 " pdb=" O4 DT M 99 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT K 35 " pdb=" C4 DT K 35 " pdb=" O4 DT K 35 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 59301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 12558 35.24 - 70.49: 1569 70.49 - 105.73: 31 105.73 - 140.98: 0 140.98 - 176.22: 3 Dihedral angle restraints: 14161 sinusoidal: 9563 harmonic: 4598 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 43.78 176.22 1 3.50e+01 8.16e-04 1.57e+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 67.76 152.24 1 3.50e+01 8.16e-04 1.48e+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 72.84 147.16 1 3.50e+01 8.16e-04 1.44e+01 ... (remaining 14158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2468 0.081 - 0.162: 376 0.162 - 0.243: 37 0.243 - 0.323: 0 0.323 - 0.404: 2 Chirality restraints: 2883 Sorted by residual: 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 -2.74 -0.40 2.00e-01 2.50e+01 4.09e+00 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 -2.72 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C3' DT K 45 " pdb=" C4' DT K 45 " pdb=" O3' DT K 45 " pdb=" C2' DT K 45 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.00e-01 ... (remaining 2880 not shown) Planarity restraints: 3759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 71 " -0.176 9.50e-02 1.11e+02 5.91e-02 4.27e+00 pdb=" NE ARG B 71 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 71 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 71 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 71 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 71 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG B 71 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 71 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 71 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG M 73 " -0.028 2.00e-02 2.50e+03 1.07e-02 4.01e+00 pdb=" N9 DG M 73 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG M 73 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG M 73 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG M 73 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG M 73 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG M 73 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG M 73 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG M 73 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG M 73 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG M 73 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG M 73 " 0.002 2.00e-02 2.50e+03 pdb=" H8 DG M 73 " 0.002 2.00e-02 2.50e+03 pdb=" H1 DG M 73 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA M 103 " 0.025 2.00e-02 2.50e+03 1.00e-02 3.27e+00 pdb=" N9 DA M 103 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA M 103 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA M 103 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA M 103 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA M 103 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA M 103 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA M 103 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA M 103 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA M 103 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA M 103 " -0.002 2.00e-02 2.50e+03 pdb=" H8 DA M 103 " -0.002 2.00e-02 2.50e+03 pdb=" H2 DA M 103 " -0.001 2.00e-02 2.50e+03 ... (remaining 3756 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 9532 2.36 - 2.92: 63931 2.92 - 3.48: 72563 3.48 - 4.04: 107660 4.04 - 4.60: 154590 Nonbonded interactions: 408276 Sorted by model distance: nonbonded pdb=" HG2 ARG B 71 " pdb="HH11 ARG B 71 " model vdw 1.796 2.270 nonbonded pdb=" HG3 ARG J 54 " pdb="HH11 ARG J 54 " model vdw 1.831 2.270 nonbonded pdb=" H VAL E 118 " pdb=" H THR E 119 " model vdw 1.841 2.100 nonbonded pdb="HE21 GLN F 69 " pdb=" HE ARG F 73 " model vdw 1.863 2.100 nonbonded pdb=" HD1 PHE P 176 " pdb="HE21 GLN P 177 " model vdw 1.868 2.100 ... (remaining 408271 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' and resid 26 through 124) 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: 1.940 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: 0.190 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.770 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 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 0.043 18150 Z= 0.502 Angle : 0.720 10.730 25810 Z= 0.584 Chirality : 0.059 0.404 2883 Planarity : 0.004 0.077 2204 Dihedral : 23.924 176.219 7575 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.19 % Allowed : 10.32 % Favored : 88.48 % 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: 1.43 (0.24), residues: 1350 helix: 2.81 (0.23), residues: 519 sheet: 0.31 (0.34), residues: 251 loop : -0.50 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 71 TYR 0.016 0.001 TYR I 73 PHE 0.012 0.001 PHE P 194 TRP 0.006 0.001 TRP I 65 HIS 0.005 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.50 (18148) covalent geometry : angle 0.71972 / 0.58 (25806) SS BOND : bond 0.00561 / 0.33 ( 2) SS BOND : angle 1.09567 / 0.52 ( 4) hydrogen bonds : bond 0.15433 / 10.31 ( 949) hydrogen bonds : angle 5.26682 / 3.78 ( 2383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.697 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 91 GLU cc_start: 0.9043 (tp30) cc_final: 0.8631 (tp30) REVERT: A 110 ASN cc_start: 0.9050 (t0) cc_final: 0.8486 (p0) REVERT: D 67 ASP cc_start: 0.9123 (t70) cc_final: 0.8693 (t0) REVERT: D 92 GLU cc_start: 0.8877 (mp0) cc_final: 0.8628 (mp0) REVERT: E 60 GLU cc_start: 0.9005 (pm20) cc_final: 0.8672 (pm20) REVERT: E 98 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8415 (mm-30) REVERT: G 65 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8182 (mt-10) REVERT: H 55 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: H 61 LYS cc_start: 0.9085 (ttpp) cc_final: 0.8837 (tttp) REVERT: H 82 THR cc_start: 0.9259 (m) cc_final: 0.9018 (p) REVERT: J 154 MET cc_start: 0.7383 (ppp) cc_final: 0.7159 (ppp) outliers start: 14 outliers final: 13 residues processed: 157 average time/residue: 0.3450 time to fit residues: 77.7224 Evaluate side-chains 155 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 40 HIS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain J residue 105 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.065801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.046312 restraints weight = 147905.111| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.29 r_work: 0.2691 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 18150 Z= 0.277 Angle : 0.628 6.018 25810 Z= 0.399 Chirality : 0.042 0.262 2883 Planarity : 0.004 0.048 2204 Dihedral : 26.877 179.156 4894 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.45 % Allowed : 10.75 % Favored : 87.80 % 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: 1.26 (0.23), residues: 1350 helix: 2.55 (0.23), residues: 526 sheet: 0.54 (0.33), residues: 263 loop : -0.70 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 71 TYR 0.017 0.001 TYR I 73 PHE 0.015 0.001 PHE P 194 TRP 0.007 0.001 TRP I 264 HIS 0.006 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.28 (18148) covalent geometry : angle 0.62803 / 0.40 (25806) SS BOND : bond 0.00856 / 0.50 ( 2) SS BOND : angle 1.64677 / 0.81 ( 4) hydrogen bonds : bond 0.06668 / 4.51 ( 949) hydrogen bonds : angle 4.30881 / 3.09 ( 2383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.791 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 91 GLU cc_start: 0.9071 (tp30) cc_final: 0.8676 (tp30) REVERT: A 110 ASN cc_start: 0.9016 (t0) cc_final: 0.8423 (p0) REVERT: D 92 GLU cc_start: 0.8812 (mp0) cc_final: 0.8531 (mp0) REVERT: E 60 GLU cc_start: 0.8893 (pm20) cc_final: 0.8495 (pm20) REVERT: E 98 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7905 (mm-30) REVERT: H 55 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: H 61 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8804 (tttp) REVERT: H 82 THR cc_start: 0.9267 (m) cc_final: 0.8986 (p) outliers start: 17 outliers final: 12 residues processed: 150 average time/residue: 0.3584 time to fit residues: 76.6035 Evaluate side-chains 152 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain F residue 40 HIS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain J residue 105 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 70 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 39 optimal weight: 0.7980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.067065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.047519 restraints weight = 146286.519| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.31 r_work: 0.2735 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18150 Z= 0.141 Angle : 0.545 6.300 25810 Z= 0.358 Chirality : 0.039 0.262 2883 Planarity : 0.004 0.047 2204 Dihedral : 26.932 178.944 4887 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.02 % Allowed : 11.01 % Favored : 87.97 % 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: 1.60 (0.24), residues: 1350 helix: 2.84 (0.22), residues: 529 sheet: 0.81 (0.34), residues: 263 loop : -0.60 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.012 0.001 TYR I 73 PHE 0.007 0.001 PHE P 176 TRP 0.008 0.001 TRP I 264 HIS 0.003 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.14 (18148) covalent geometry : angle 0.54461 / 0.36 (25806) SS BOND : bond 0.00616 / 0.36 ( 2) SS BOND : angle 1.12840 / 0.58 ( 4) hydrogen bonds : bond 0.05426 / 3.69 ( 949) hydrogen bonds : angle 3.82765 / 2.75 ( 2383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.9023 (tp30) cc_final: 0.8682 (tp30) REVERT: A 110 ASN cc_start: 0.8963 (t0) cc_final: 0.8371 (p0) REVERT: D 67 ASP cc_start: 0.8975 (t70) cc_final: 0.8629 (t0) REVERT: D 92 GLU cc_start: 0.8746 (mp0) cc_final: 0.8463 (mp0) REVERT: E 60 GLU cc_start: 0.8791 (pm20) cc_final: 0.8527 (pm20) REVERT: E 98 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7983 (mm-30) REVERT: H 55 GLU cc_start: 0.8794 (mp0) cc_final: 0.8310 (mp0) REVERT: H 61 LYS cc_start: 0.8974 (ttpp) cc_final: 0.8728 (tttp) REVERT: H 82 THR cc_start: 0.9275 (m) cc_final: 0.8990 (p) outliers start: 12 outliers final: 8 residues processed: 158 average time/residue: 0.3397 time to fit residues: 77.2630 Evaluate side-chains 153 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain J residue 156 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.067640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.048142 restraints weight = 146411.964| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.32 r_work: 0.2750 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18150 Z= 0.138 Angle : 0.534 6.263 25810 Z= 0.348 Chirality : 0.038 0.259 2883 Planarity : 0.004 0.058 2204 Dihedral : 26.971 178.583 4878 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.77 % Allowed : 11.01 % Favored : 88.23 % 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: 1.90 (0.24), residues: 1350 helix: 3.09 (0.23), residues: 531 sheet: 1.06 (0.33), residues: 277 loop : -0.54 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.011 0.001 TYR I 73 PHE 0.007 0.001 PHE P 194 TRP 0.008 0.001 TRP I 264 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.14 (18148) covalent geometry : angle 0.53426 / 0.35 (25806) SS BOND : bond 0.00593 / 0.34 ( 2) SS BOND : angle 1.00164 / 0.52 ( 4) hydrogen bonds : bond 0.04776 / 3.25 ( 949) hydrogen bonds : angle 3.52636 / 2.55 ( 2383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8986 (tp30) cc_final: 0.8625 (tp30) REVERT: A 110 ASN cc_start: 0.8970 (t0) cc_final: 0.8364 (p0) REVERT: D 67 ASP cc_start: 0.8947 (t70) cc_final: 0.8611 (t0) REVERT: D 92 GLU cc_start: 0.8714 (mp0) cc_final: 0.8376 (mp0) REVERT: G 65 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8086 (mt-10) REVERT: H 55 GLU cc_start: 0.8783 (mp0) cc_final: 0.8329 (mp0) REVERT: H 61 LYS cc_start: 0.8943 (ttpp) cc_final: 0.8685 (tttp) REVERT: H 82 THR cc_start: 0.9277 (m) cc_final: 0.9011 (p) REVERT: P 190 ASP cc_start: 0.9052 (m-30) cc_final: 0.8337 (t0) REVERT: J 154 MET cc_start: 0.7520 (ppp) cc_final: 0.7187 (ppp) REVERT: I 42 ARG cc_start: 0.8633 (tmm-80) cc_final: 0.8223 (ttp80) outliers start: 9 outliers final: 8 residues processed: 158 average time/residue: 0.3264 time to fit residues: 74.4857 Evaluate side-chains 156 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 36 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 73 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.067183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.047665 restraints weight = 147261.740| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.32 r_work: 0.2733 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18150 Z= 0.178 Angle : 0.548 6.293 25810 Z= 0.353 Chirality : 0.038 0.256 2883 Planarity : 0.004 0.056 2204 Dihedral : 27.037 178.929 4877 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.19 % Allowed : 11.86 % Favored : 86.95 % 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: 1.85 (0.24), residues: 1350 helix: 3.08 (0.22), residues: 531 sheet: 0.99 (0.33), residues: 277 loop : -0.60 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.013 0.001 TYR I 73 PHE 0.009 0.001 PHE P 194 TRP 0.007 0.001 TRP I 264 HIS 0.005 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 (18148) covalent geometry : angle 0.54767 / 0.35 (25806) SS BOND : bond 0.00674 / 0.39 ( 2) SS BOND : angle 1.19851 / 0.61 ( 4) hydrogen bonds : bond 0.04984 / 3.38 ( 949) hydrogen bonds : angle 3.52787 / 2.54 ( 2383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.749 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 91 GLU cc_start: 0.9036 (tp30) cc_final: 0.8658 (tp30) REVERT: A 110 ASN cc_start: 0.8980 (t0) cc_final: 0.8374 (p0) REVERT: D 67 ASP cc_start: 0.8953 (t70) cc_final: 0.8604 (t0) REVERT: D 92 GLU cc_start: 0.8750 (mp0) cc_final: 0.8398 (mp0) REVERT: E 60 GLU cc_start: 0.8761 (pm20) cc_final: 0.8389 (pm20) REVERT: H 55 GLU cc_start: 0.8804 (mp0) cc_final: 0.8334 (mp0) REVERT: H 61 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8713 (tttp) REVERT: H 82 THR cc_start: 0.9296 (m) cc_final: 0.9002 (p) REVERT: J 154 MET cc_start: 0.7522 (ppp) cc_final: 0.7185 (ppp) outliers start: 14 outliers final: 12 residues processed: 156 average time/residue: 0.3407 time to fit residues: 76.6698 Evaluate side-chains 156 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain F residue 40 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain I residue 36 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 112 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.067598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.047993 restraints weight = 146552.458| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.37 r_work: 0.2742 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18150 Z= 0.143 Angle : 0.534 6.440 25810 Z= 0.346 Chirality : 0.038 0.257 2883 Planarity : 0.004 0.062 2204 Dihedral : 27.070 178.924 4877 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.28 % Allowed : 12.12 % Favored : 86.60 % 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: 1.94 (0.24), residues: 1350 helix: 3.15 (0.22), residues: 532 sheet: 1.04 (0.33), residues: 277 loop : -0.55 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 71 TYR 0.012 0.001 TYR I 73 PHE 0.007 0.001 PHE P 194 TRP 0.006 0.001 TRP I 264 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (18148) covalent geometry : angle 0.53344 / 0.35 (25806) SS BOND : bond 0.00594 / 0.34 ( 2) SS BOND : angle 1.00874 / 0.52 ( 4) hydrogen bonds : bond 0.04725 / 3.21 ( 949) hydrogen bonds : angle 3.39696 / 2.45 ( 2383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.753 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 91 GLU cc_start: 0.8972 (tp30) cc_final: 0.8597 (tp30) REVERT: A 110 ASN cc_start: 0.8967 (t0) cc_final: 0.8384 (p0) REVERT: C 112 GLU cc_start: 0.9084 (tp30) cc_final: 0.8735 (tp30) REVERT: D 67 ASP cc_start: 0.8925 (t70) cc_final: 0.8564 (t0) REVERT: D 92 GLU cc_start: 0.8704 (mp0) cc_final: 0.8385 (mp0) REVERT: E 60 GLU cc_start: 0.8750 (pm20) cc_final: 0.8359 (pm20) REVERT: G 65 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8096 (mt-10) REVERT: H 55 GLU cc_start: 0.8777 (mp0) cc_final: 0.8335 (mp0) REVERT: H 61 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8732 (tttp) REVERT: H 82 THR cc_start: 0.9301 (m) cc_final: 0.9028 (p) REVERT: P 117 VAL cc_start: 0.9093 (t) cc_final: 0.8854 (p) REVERT: J 154 MET cc_start: 0.7542 (ppp) cc_final: 0.7192 (ppp) outliers start: 15 outliers final: 12 residues processed: 159 average time/residue: 0.3317 time to fit residues: 76.3033 Evaluate side-chains 158 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain F residue 40 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain I residue 36 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.067576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.048107 restraints weight = 147300.830| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.33 r_work: 0.2747 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18150 Z= 0.151 Angle : 0.535 6.329 25810 Z= 0.346 Chirality : 0.038 0.258 2883 Planarity : 0.004 0.068 2204 Dihedral : 27.093 179.022 4877 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.28 % Allowed : 12.03 % Favored : 86.69 % 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: 1.93 (0.24), residues: 1350 helix: 3.13 (0.22), residues: 535 sheet: 1.04 (0.33), residues: 277 loop : -0.55 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 71 TYR 0.012 0.001 TYR I 73 PHE 0.008 0.001 PHE P 194 TRP 0.006 0.001 TRP I 264 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (18148) covalent geometry : angle 0.53536 / 0.35 (25806) SS BOND : bond 0.00619 / 0.36 ( 2) SS BOND : angle 1.05276 / 0.54 ( 4) hydrogen bonds : bond 0.04677 / 3.18 ( 949) hydrogen bonds : angle 3.34757 / 2.41 ( 2383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8996 (tp30) cc_final: 0.8593 (tp30) REVERT: A 110 ASN cc_start: 0.8968 (t0) cc_final: 0.8373 (p0) REVERT: C 112 GLU cc_start: 0.9100 (tp30) cc_final: 0.8776 (tp30) REVERT: D 67 ASP cc_start: 0.8942 (t70) cc_final: 0.8574 (t0) REVERT: D 92 GLU cc_start: 0.8720 (mp0) cc_final: 0.8380 (mp0) REVERT: E 60 GLU cc_start: 0.8744 (pm20) cc_final: 0.8330 (pm20) REVERT: E 98 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7955 (mm-30) REVERT: H 55 GLU cc_start: 0.8787 (mp0) cc_final: 0.8334 (mp0) REVERT: H 61 LYS cc_start: 0.8943 (ttpp) cc_final: 0.8706 (tttp) REVERT: H 82 THR cc_start: 0.9319 (m) cc_final: 0.9019 (p) REVERT: P 117 VAL cc_start: 0.9081 (t) cc_final: 0.8846 (p) REVERT: J 154 MET cc_start: 0.7533 (ppp) cc_final: 0.7171 (ppp) outliers start: 15 outliers final: 13 residues processed: 158 average time/residue: 0.3288 time to fit residues: 74.7882 Evaluate side-chains 159 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain F residue 40 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain I residue 36 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 87 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.068077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.048576 restraints weight = 147114.206| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.33 r_work: 0.2764 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18150 Z= 0.130 Angle : 0.526 6.588 25810 Z= 0.340 Chirality : 0.038 0.258 2883 Planarity : 0.004 0.078 2204 Dihedral : 27.107 178.819 4877 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.11 % Allowed : 12.54 % Favored : 86.35 % 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: 2.03 (0.24), residues: 1350 helix: 3.23 (0.23), residues: 535 sheet: 1.10 (0.33), residues: 277 loop : -0.53 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 71 TYR 0.010 0.001 TYR I 73 PHE 0.006 0.001 PHE P 194 TRP 0.006 0.001 TRP I 264 HIS 0.002 0.000 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.13 (18148) covalent geometry : angle 0.52582 / 0.34 (25806) SS BOND : bond 0.00518 / 0.30 ( 2) SS BOND : angle 0.90572 / 0.47 ( 4) hydrogen bonds : bond 0.04369 / 2.97 ( 949) hydrogen bonds : angle 3.22481 / 2.32 ( 2383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8984 (tp30) cc_final: 0.8574 (tp30) REVERT: A 110 ASN cc_start: 0.8948 (t0) cc_final: 0.8348 (p0) REVERT: C 112 GLU cc_start: 0.9080 (tp30) cc_final: 0.8789 (tp30) REVERT: D 67 ASP cc_start: 0.8923 (t70) cc_final: 0.8579 (t0) REVERT: D 92 GLU cc_start: 0.8696 (mp0) cc_final: 0.8355 (mp0) REVERT: E 60 GLU cc_start: 0.8718 (pm20) cc_final: 0.8465 (pm20) REVERT: E 98 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7953 (mm-30) REVERT: G 65 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8084 (mt-10) REVERT: H 55 GLU cc_start: 0.8759 (mp0) cc_final: 0.8238 (mp0) REVERT: H 61 LYS cc_start: 0.8915 (ttpp) cc_final: 0.8659 (tttp) REVERT: H 82 THR cc_start: 0.9327 (m) cc_final: 0.9052 (p) REVERT: P 117 VAL cc_start: 0.9063 (t) cc_final: 0.8829 (p) REVERT: P 190 ASP cc_start: 0.9041 (m-30) cc_final: 0.8345 (t0) REVERT: J 154 MET cc_start: 0.7538 (ppp) cc_final: 0.7168 (ppp) REVERT: J 196 ARG cc_start: 0.8523 (ttp-110) cc_final: 0.8242 (ttp-110) outliers start: 13 outliers final: 10 residues processed: 160 average time/residue: 0.3077 time to fit residues: 71.1842 Evaluate side-chains 158 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain F residue 40 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain J residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 133 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.068675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049113 restraints weight = 146275.119| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.38 r_work: 0.2779 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18150 Z= 0.124 Angle : 0.522 6.489 25810 Z= 0.337 Chirality : 0.038 0.257 2883 Planarity : 0.004 0.083 2204 Dihedral : 27.103 178.412 4877 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.68 % Allowed : 12.88 % Favored : 86.43 % 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: 2.15 (0.24), residues: 1350 helix: 3.31 (0.23), residues: 539 sheet: 1.20 (0.33), residues: 277 loop : -0.49 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 71 TYR 0.008 0.001 TYR I 73 PHE 0.005 0.001 PHE I 95 TRP 0.006 0.001 TRP I 264 HIS 0.002 0.000 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.12 (18148) covalent geometry : angle 0.52186 / 0.34 (25806) SS BOND : bond 0.00498 / 0.29 ( 2) SS BOND : angle 0.82936 / 0.42 ( 4) hydrogen bonds : bond 0.04076 / 2.77 ( 949) hydrogen bonds : angle 3.11229 / 2.24 ( 2383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.675 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 91 GLU cc_start: 0.8945 (tp30) cc_final: 0.8516 (tp30) REVERT: A 110 ASN cc_start: 0.8947 (t0) cc_final: 0.8362 (p0) REVERT: C 112 GLU cc_start: 0.9059 (tp30) cc_final: 0.8775 (tp30) REVERT: D 67 ASP cc_start: 0.8894 (t70) cc_final: 0.8517 (t0) REVERT: D 92 GLU cc_start: 0.8665 (mp0) cc_final: 0.8315 (mp0) REVERT: E 60 GLU cc_start: 0.8721 (pm20) cc_final: 0.8466 (pm20) REVERT: H 55 GLU cc_start: 0.8701 (mp0) cc_final: 0.8204 (mp0) REVERT: H 61 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8667 (tttp) REVERT: H 82 THR cc_start: 0.9316 (m) cc_final: 0.9064 (p) REVERT: P 190 ASP cc_start: 0.9027 (m-30) cc_final: 0.8329 (t0) REVERT: J 154 MET cc_start: 0.7553 (ppp) cc_final: 0.7182 (ppp) REVERT: J 196 ARG cc_start: 0.8523 (ttp-110) cc_final: 0.8250 (ttp-110) outliers start: 8 outliers final: 7 residues processed: 159 average time/residue: 0.3122 time to fit residues: 71.5986 Evaluate side-chains 152 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain J residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 62 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.067804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.048300 restraints weight = 147883.244| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.32 r_work: 0.2755 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18150 Z= 0.175 Angle : 0.545 6.088 25810 Z= 0.347 Chirality : 0.038 0.258 2883 Planarity : 0.004 0.078 2204 Dihedral : 27.144 178.879 4875 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.94 % Allowed : 13.05 % Favored : 86.01 % 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: 2.07 (0.24), residues: 1350 helix: 3.27 (0.23), residues: 536 sheet: 1.17 (0.33), residues: 277 loop : -0.56 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 71 TYR 0.013 0.001 TYR I 73 PHE 0.008 0.001 PHE P 194 TRP 0.004 0.001 TRP J 264 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.18 (18148) covalent geometry : angle 0.54533 / 0.35 (25806) SS BOND : bond 0.00653 / 0.38 ( 2) SS BOND : angle 1.20501 / 0.61 ( 4) hydrogen bonds : bond 0.04510 / 3.06 ( 949) hydrogen bonds : angle 3.20446 / 2.30 ( 2383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.695 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: symmetry clash REVERT: A 91 GLU cc_start: 0.9020 (tp30) cc_final: 0.8596 (tp30) REVERT: A 110 ASN cc_start: 0.8972 (t0) cc_final: 0.8368 (p0) REVERT: C 112 GLU cc_start: 0.9107 (tp30) cc_final: 0.8840 (tp30) REVERT: D 67 ASP cc_start: 0.8947 (t70) cc_final: 0.8592 (t0) REVERT: D 92 GLU cc_start: 0.8730 (mp0) cc_final: 0.8306 (mp0) REVERT: H 55 GLU cc_start: 0.8795 (mp0) cc_final: 0.8247 (mp0) REVERT: H 61 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8705 (tttp) REVERT: H 82 THR cc_start: 0.9329 (m) cc_final: 0.9034 (p) REVERT: J 154 MET cc_start: 0.7557 (ppp) cc_final: 0.7191 (ppp) REVERT: J 196 ARG cc_start: 0.8537 (ttp-110) cc_final: 0.8260 (ttp-110) outliers start: 11 outliers final: 11 residues processed: 153 average time/residue: 0.3113 time to fit residues: 68.7678 Evaluate side-chains 156 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain J residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.067479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.047939 restraints weight = 147186.807| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.31 r_work: 0.2747 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18150 Z= 0.174 Angle : 0.547 6.519 25810 Z= 0.348 Chirality : 0.038 0.260 2883 Planarity : 0.004 0.077 2204 Dihedral : 27.214 179.573 4875 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.94 % Allowed : 13.14 % Favored : 85.92 % 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: 2.00 (0.24), residues: 1350 helix: 3.18 (0.22), residues: 536 sheet: 1.14 (0.33), residues: 277 loop : -0.56 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 71 TYR 0.013 0.001 TYR I 73 PHE 0.009 0.001 PHE P 194 TRP 0.005 0.001 TRP I 264 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (18148) covalent geometry : angle 0.54703 / 0.35 (25806) SS BOND : bond 0.00627 / 0.36 ( 2) SS BOND : angle 1.19725 / 0.60 ( 4) hydrogen bonds : bond 0.04711 / 3.19 ( 949) hydrogen bonds : angle 3.24173 / 2.33 ( 2383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6644.97 seconds wall clock time: 113 minutes 24.38 seconds (6804.38 seconds total)