Starting phenix.real_space_refine on Thu Aug 6 06:54:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g57_29735/08_2026/8g57_29735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g57_29735/08_2026/8g57_29735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g57_29735/08_2026/8g57_29735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g57_29735/08_2026/8g57_29735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g57_29735/08_2026/8g57_29735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g57_29735/08_2026/8g57_29735.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.395 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: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 22 5.16 5 C 8104 2.51 5 N 2706 2.21 5 O 3270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 14402 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 2037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2037 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'TRP:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 867 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 846 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 740 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 874 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 739 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3093 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3057 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N LEU B 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 22 " occ=0.00 residue: pdb=" N ARG B 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 23 " occ=0.00 residue: pdb=" N LYS C 13 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS C 13 " occ=0.00 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 residue: pdb=" N ARG G 11 " occ=0.00 ... (3 atoms not shown) pdb=" CB ARG G 11 " occ=0.00 residue: pdb=" N ALA G 12 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 12 " occ=0.00 Time building chain proxies: 2.72, per 1000 atoms: 0.19 Number of scatterers: 14402 At special positions: 0 Unit cell: (113.4, 141.48, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 300 15.00 O 3270 8.00 N 2706 7.00 C 8104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 363.2 milliseconds 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 11 sheets defined 60.0% alpha, 4.7% beta 149 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'K' and resid 27 through 43 removed outlier: 3.828A pdb=" N GLU K 31 " --> pdb=" O PRO K 27 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG K 32 " --> pdb=" O GLU K 28 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP K 42 " --> pdb=" O ALA K 38 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 60 removed outlier: 4.395A pdb=" N ALA K 58 " --> pdb=" O ILE K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 Processing helix chain 'K' and resid 82 through 87 Processing helix chain 'K' and resid 92 through 105 removed outlier: 3.579A pdb=" N GLN K 100 " --> pdb=" O MET K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 122 Processing helix chain 'K' and resid 125 through 127 No H-bonds generated for 'chain 'K' and resid 125 through 127' Processing helix chain 'K' and resid 193 through 206 Processing helix chain 'K' and resid 223 through 232 removed outlier: 4.648A pdb=" N LEU K 227 " --> pdb=" O GLY K 223 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR K 229 " --> pdb=" O LEU K 225 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS K 230 " --> pdb=" O PRO K 226 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG K 231 " --> pdb=" O LEU K 227 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 removed outlier: 4.147A pdb=" N THR K 263 " --> pdb=" O ASP K 259 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG K 264 " --> pdb=" O GLU K 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS K 268 " --> pdb=" O ARG K 264 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU K 269 " --> pdb=" O LEU K 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.582A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 74 removed outlier: 3.609A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.619A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.675A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 125 removed outlier: 3.592A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.615A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.604A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.584A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.678A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.966A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.596A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.894A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.569A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.518A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 52 through 80 removed outlier: 3.677A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.532A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 Processing sheet with id=AA1, first strand: chain 'K' and resid 129 through 131 removed outlier: 6.454A pdb=" N VAL K 47 " --> pdb=" O PHE K 109 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL K 111 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE K 49 " --> pdb=" O VAL K 111 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE K 211 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER K 210 " --> pdb=" O VAL K 237 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL K 239 " --> pdb=" O SER K 210 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR K 212 " --> pdb=" O VAL K 239 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE K 238 " --> pdb=" O ILE K 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 147 through 149 removed outlier: 7.715A pdb=" N LEU K 181 " --> pdb=" O THR K 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.634A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.045A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.556A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.876A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 443 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 381 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 149 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2942 1.33 - 1.45: 4639 1.45 - 1.57: 7049 1.57 - 1.69: 597 1.69 - 1.81: 37 Bond restraints: 15264 Sorted by residual: bond pdb=" C1' DT I 171 " pdb=" N1 DT I 171 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.08e+01 bond pdb=" C1' DC J 3 " pdb=" N1 DC J 3 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.08e+01 bond pdb=" C1' DG I 169 " pdb=" N9 DG I 169 " ideal model delta sigma weight residual 1.468 1.397 0.071 1.40e-02 5.10e+03 2.61e+01 bond pdb=" C1' DA J 1 " pdb=" N9 DA J 1 " ideal model delta sigma weight residual 1.468 1.398 0.070 1.40e-02 5.10e+03 2.50e+01 bond pdb=" CE1 HIS K 249 " pdb=" NE2 HIS K 249 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.68e+01 ... (remaining 15259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21127 2.09 - 4.19: 759 4.19 - 6.28: 20 6.28 - 8.38: 9 8.38 - 10.47: 2 Bond angle restraints: 21917 Sorted by residual: angle pdb=" C ALA K 250 " pdb=" CA ALA K 250 " pdb=" CB ALA K 250 " ideal model delta sigma weight residual 116.53 108.70 7.83 1.47e+00 4.63e-01 2.84e+01 angle pdb=" O ALA K 250 " pdb=" C ALA K 250 " pdb=" N ASP K 251 " ideal model delta sigma weight residual 121.65 125.55 -3.90 8.30e-01 1.45e+00 2.21e+01 angle pdb=" O4' DT I 111 " pdb=" C4' DT I 111 " pdb=" C3' DT I 111 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" O4' DA I 126 " pdb=" C4' DA I 126 " pdb=" C3' DA I 126 " ideal model delta sigma weight residual 106.00 103.32 2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT I 39 " pdb=" C4 DT I 39 " pdb=" O4 DT I 39 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 21912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 7009 34.44 - 68.88: 1403 68.88 - 103.32: 10 103.32 - 137.77: 1 137.77 - 172.21: 1 Dihedral angle restraints: 8424 sinusoidal: 5349 harmonic: 3075 Sorted by residual: dihedral pdb=" CA PRO K 287 " pdb=" C PRO K 287 " pdb=" N PRO K 288 " pdb=" CA PRO K 288 " ideal model delta harmonic sigma weight residual -180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C4' DT J 115 " pdb=" C3' DT J 115 " pdb=" O3' DT J 115 " pdb=" P DC J 116 " ideal model delta sinusoidal sigma weight residual 220.00 47.79 172.21 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1954 0.053 - 0.106: 491 0.106 - 0.158: 57 0.158 - 0.211: 3 0.211 - 0.264: 3 Chirality restraints: 2508 Sorted by residual: chirality pdb=" CA PRO K 288 " pdb=" N PRO K 288 " pdb=" C PRO K 288 " pdb=" CB PRO K 288 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA GLU K 202 " pdb=" N GLU K 202 " pdb=" C GLU K 202 " pdb=" CB GLU K 202 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO A 38 " pdb=" N PRO A 38 " pdb=" C PRO A 38 " pdb=" CB PRO A 38 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2505 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 287 " 0.080 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO K 288 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO K 288 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO K 288 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 289 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO K 290 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO K 290 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO K 290 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO A 43 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.032 5.00e-02 4.00e+02 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 12 2.33 - 2.97: 6043 2.97 - 3.61: 21507 3.61 - 4.26: 36856 4.26 - 4.90: 54275 Nonbonded interactions: 118693 Sorted by model distance: nonbonded pdb=" NH2 ARG K 220 " pdb=" O GLY A 12 " model vdw 1.682 3.120 nonbonded pdb=" NE ARG K 220 " pdb=" O THR A 11 " model vdw 1.976 3.120 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.113 3.040 nonbonded pdb=" N2 DG I 79 " pdb=" O2 DC J 93 " model vdw 2.189 2.496 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.237 3.040 ... (remaining 118688 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' and resid 36 through 134) selection = (chain 'E' and ((resid 36 through 39 and (name N or name CA or name C or name O \ or name CB )) or resid 40 through 133 or (resid 134 and (name N or name CA or na \ me C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 19 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 102)) selection = (chain 'F' and ((resid 19 through 21 and (name N or name CA or name C or name O \ or name CB )) or resid 22 through 102)) } ncs_group { reference = (chain 'C' and ((resid 11 through 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 120)) selection = (chain 'G' and resid 11 through 120) } ncs_group { reference = (chain 'D' and resid 31 through 125) selection = (chain 'H' and (resid 28 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB )))) } 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=0.00 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 0.078 15264 Z= 0.502 Angle : 0.789 10.470 21917 Z= 0.666 Chirality : 0.046 0.264 2508 Planarity : 0.006 0.124 1749 Dihedral : 25.922 172.206 6436 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.86 % Allowed : 3.07 % Favored : 96.07 % Rotamer: Outliers : 0.12 % Allowed : 0.59 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 1043 helix: 1.23 (0.22), residues: 599 sheet: -2.10 (0.82), residues: 42 loop : -1.91 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 92 TYR 0.016 0.001 TYR F 88 PHE 0.010 0.001 PHE C 25 TRP 0.023 0.002 TRP K 35 HIS 0.003 0.001 HIS K 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.50 (15264) covalent geometry : angle 0.78886 / 0.67 (21917) hydrogen bonds : bond 0.11876 / 7.95 ( 824) hydrogen bonds : angle 4.42337 / 3.05 ( 2060) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 0.280 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8265 (tt0) cc_final: 0.7712 (tt0) REVERT: A 107 THR cc_start: 0.9464 (m) cc_final: 0.9212 (m) REVERT: B 27 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8753 (mm-40) REVERT: B 68 ASP cc_start: 0.8574 (m-30) cc_final: 0.8321 (m-30) REVERT: B 77 LYS cc_start: 0.9321 (mmtp) cc_final: 0.9059 (mmtm) REVERT: D 68 ASP cc_start: 0.8570 (t70) cc_final: 0.7925 (t0) REVERT: D 85 LYS cc_start: 0.9349 (mmtm) cc_final: 0.9032 (mmtt) REVERT: E 90 MET cc_start: 0.8600 (mmp) cc_final: 0.8369 (mmm) REVERT: F 45 ARG cc_start: 0.8691 (ttt90) cc_final: 0.8445 (ttt90) REVERT: G 15 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8618 (mtpp) REVERT: G 76 THR cc_start: 0.9131 (p) cc_final: 0.8889 (t) REVERT: G 90 ASP cc_start: 0.8440 (t0) cc_final: 0.8205 (t0) REVERT: H 65 ASP cc_start: 0.8946 (t0) cc_final: 0.8713 (t0) REVERT: H 105 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7701 (mtmt) outliers start: 1 outliers final: 0 residues processed: 354 average time/residue: 0.1409 time to fit residues: 66.7109 Evaluate side-chains 294 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN ** K 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN B 93 GLN D 49 HIS F 27 GLN G 73 ASN H 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.092552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.057171 restraints weight = 32777.583| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.07 r_work: 0.2546 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15264 Z= 0.282 Angle : 0.742 12.876 21917 Z= 0.410 Chirality : 0.048 0.316 2508 Planarity : 0.006 0.129 1749 Dihedral : 29.657 174.070 4453 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.67 % Allowed : 3.64 % Favored : 95.69 % Rotamer: Outliers : 2.26 % Allowed : 10.82 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.27), residues: 1043 helix: 1.47 (0.22), residues: 616 sheet: -2.08 (0.92), residues: 36 loop : -1.87 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 220 TYR 0.019 0.002 TYR F 51 PHE 0.022 0.002 PHE K 109 TRP 0.010 0.002 TRP K 35 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.28 (15264) covalent geometry : angle 0.74210 / 0.41 (21917) hydrogen bonds : bond 0.06037 / 4.13 ( 824) hydrogen bonds : angle 3.29128 / 2.31 ( 2060) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 296 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 95 HIS cc_start: 0.9322 (m90) cc_final: 0.9030 (m90) REVERT: K 96 MET cc_start: 0.9040 (mpp) cc_final: 0.8760 (mpp) REVERT: K 100 GLN cc_start: 0.9242 (tt0) cc_final: 0.8857 (tt0) REVERT: K 124 PHE cc_start: 0.8682 (t80) cc_final: 0.8432 (t80) REVERT: K 132 LEU cc_start: 0.9509 (mm) cc_final: 0.9287 (mm) REVERT: K 135 ASN cc_start: 0.8910 (t0) cc_final: 0.8702 (t0) REVERT: K 140 GLU cc_start: 0.8856 (tp30) cc_final: 0.8607 (tp30) REVERT: K 204 SER cc_start: 0.9401 (m) cc_final: 0.9187 (p) REVERT: K 246 HIS cc_start: 0.8746 (m90) cc_final: 0.8424 (m90) REVERT: A 4 LYS cc_start: 0.8583 (ptpt) cc_final: 0.8231 (ptpp) REVERT: A 59 GLU cc_start: 0.9018 (pm20) cc_final: 0.8817 (pm20) REVERT: A 73 GLU cc_start: 0.8872 (tt0) cc_final: 0.8445 (tt0) REVERT: A 76 GLN cc_start: 0.9119 (pp30) cc_final: 0.8898 (pp30) REVERT: B 27 GLN cc_start: 0.9266 (mm-40) cc_final: 0.9010 (mm-40) REVERT: C 99 ARG cc_start: 0.9036 (ptp90) cc_final: 0.8758 (ptp-110) REVERT: D 68 ASP cc_start: 0.9045 (t70) cc_final: 0.8506 (t0) REVERT: D 85 LYS cc_start: 0.9445 (mmtm) cc_final: 0.9194 (mmtt) REVERT: D 93 GLU cc_start: 0.8926 (mp0) cc_final: 0.8706 (mp0) REVERT: E 129 ARG cc_start: 0.9007 (tpp80) cc_final: 0.8715 (tpt-90) REVERT: F 67 ARG cc_start: 0.9067 (ttp-110) cc_final: 0.8836 (ttp80) REVERT: G 15 LYS cc_start: 0.8309 (mtpt) cc_final: 0.8082 (mtpp) REVERT: G 74 LYS cc_start: 0.9560 (mmtt) cc_final: 0.9228 (mmmm) REVERT: H 102 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8421 (mm-30) REVERT: H 105 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8391 (mtmt) outliers start: 19 outliers final: 15 residues processed: 305 average time/residue: 0.1352 time to fit residues: 55.1936 Evaluate side-chains 297 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 282 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN E 125 GLN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.093865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.058350 restraints weight = 33432.475| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.10 r_work: 0.2579 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15264 Z= 0.174 Angle : 0.654 11.867 21917 Z= 0.367 Chirality : 0.045 0.312 2508 Planarity : 0.006 0.133 1749 Dihedral : 29.723 175.140 4453 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.16 % Favored : 96.26 % Rotamer: Outliers : 2.14 % Allowed : 13.91 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.27), residues: 1043 helix: 1.80 (0.22), residues: 613 sheet: -1.78 (0.96), residues: 36 loop : -1.76 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 231 TYR 0.012 0.001 TYR F 51 PHE 0.009 0.001 PHE K 109 TRP 0.009 0.001 TRP K 35 HIS 0.005 0.001 HIS K 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (15264) covalent geometry : angle 0.65382 / 0.37 (21917) hydrogen bonds : bond 0.05183 / 3.58 ( 824) hydrogen bonds : angle 3.06282 / 2.15 ( 2060) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 301 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 95 HIS cc_start: 0.9178 (m90) cc_final: 0.8913 (m90) REVERT: K 100 GLN cc_start: 0.9187 (tt0) cc_final: 0.8728 (tt0) REVERT: K 140 GLU cc_start: 0.8688 (tp30) cc_final: 0.8151 (tp30) REVERT: K 245 LYS cc_start: 0.8967 (pttt) cc_final: 0.8745 (pttt) REVERT: A 73 GLU cc_start: 0.8840 (tt0) cc_final: 0.8462 (tt0) REVERT: A 76 GLN cc_start: 0.9134 (pp30) cc_final: 0.8811 (pp30) REVERT: B 27 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8966 (mm-40) REVERT: B 93 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8688 (mm-40) REVERT: C 99 ARG cc_start: 0.9018 (ptp90) cc_final: 0.8805 (ptp-110) REVERT: D 68 ASP cc_start: 0.9035 (t70) cc_final: 0.8515 (t0) REVERT: D 85 LYS cc_start: 0.9447 (mmtm) cc_final: 0.9180 (mmtt) REVERT: E 129 ARG cc_start: 0.8993 (tpp80) cc_final: 0.8738 (tpt-90) REVERT: E 133 GLU cc_start: 0.8272 (mp0) cc_final: 0.8017 (mp0) REVERT: F 67 ARG cc_start: 0.9050 (ttp-110) cc_final: 0.8831 (ttp80) REVERT: G 15 LYS cc_start: 0.8255 (mtpt) cc_final: 0.8035 (mtpp) REVERT: G 74 LYS cc_start: 0.9521 (mmtt) cc_final: 0.9218 (mmmm) REVERT: G 104 GLN cc_start: 0.8941 (mm110) cc_final: 0.8697 (mm110) REVERT: H 87 THR cc_start: 0.9523 (p) cc_final: 0.9313 (t) REVERT: H 102 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7751 (mm-30) outliers start: 18 outliers final: 14 residues processed: 308 average time/residue: 0.1214 time to fit residues: 50.9046 Evaluate side-chains 297 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 283 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 102 optimal weight: 30.0000 chunk 67 optimal weight: 0.0670 chunk 126 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 242 GLN K 268 HIS E 125 GLN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.094748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.059769 restraints weight = 33080.123| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.15 r_work: 0.2602 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15264 Z= 0.139 Angle : 0.624 14.588 21917 Z= 0.351 Chirality : 0.043 0.309 2508 Planarity : 0.005 0.133 1749 Dihedral : 29.732 176.234 4453 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.26 % Favored : 96.16 % Rotamer: Outliers : 2.14 % Allowed : 14.74 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.27), residues: 1043 helix: 1.95 (0.22), residues: 612 sheet: -1.59 (0.95), residues: 36 loop : -1.75 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.009 0.001 TYR F 51 PHE 0.011 0.001 PHE K 109 TRP 0.009 0.001 TRP K 42 HIS 0.005 0.001 HIS K 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (15264) covalent geometry : angle 0.62422 / 0.35 (21917) hydrogen bonds : bond 0.04725 / 3.29 ( 824) hydrogen bonds : angle 2.90232 / 2.02 ( 2060) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 299 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 95 HIS cc_start: 0.9099 (m90) cc_final: 0.8805 (m90) REVERT: K 100 GLN cc_start: 0.9183 (tt0) cc_final: 0.8800 (tt0) REVERT: K 140 GLU cc_start: 0.8644 (tp30) cc_final: 0.8307 (tp30) REVERT: K 245 LYS cc_start: 0.8842 (pttt) cc_final: 0.8221 (ptpp) REVERT: A 73 GLU cc_start: 0.8884 (tt0) cc_final: 0.8516 (tt0) REVERT: A 76 GLN cc_start: 0.9151 (pp30) cc_final: 0.8915 (pp30) REVERT: C 36 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8998 (mtmm) REVERT: C 99 ARG cc_start: 0.8998 (ptp90) cc_final: 0.8739 (ptp-110) REVERT: D 33 ARG cc_start: 0.8351 (mtp85) cc_final: 0.7528 (mtt-85) REVERT: D 68 ASP cc_start: 0.9042 (t70) cc_final: 0.8504 (t0) REVERT: D 85 LYS cc_start: 0.9460 (mmtm) cc_final: 0.9180 (mmtt) REVERT: E 129 ARG cc_start: 0.9029 (tpp80) cc_final: 0.8712 (tpt-90) REVERT: F 67 ARG cc_start: 0.9036 (ttp-110) cc_final: 0.8812 (ttp80) REVERT: G 15 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7787 (mtpp) REVERT: G 74 LYS cc_start: 0.9556 (mmtt) cc_final: 0.9233 (mmmm) REVERT: H 87 THR cc_start: 0.9497 (p) cc_final: 0.9266 (t) outliers start: 18 outliers final: 11 residues processed: 306 average time/residue: 0.1236 time to fit residues: 51.6279 Evaluate side-chains 295 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 283 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 4 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 80 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.059968 restraints weight = 33247.172| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.16 r_work: 0.2609 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15264 Z= 0.139 Angle : 0.633 12.681 21917 Z= 0.350 Chirality : 0.043 0.310 2508 Planarity : 0.005 0.133 1749 Dihedral : 29.739 176.731 4453 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.45 % Favored : 96.07 % Rotamer: Outliers : 2.02 % Allowed : 16.53 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.27), residues: 1043 helix: 2.05 (0.22), residues: 614 sheet: -1.45 (0.95), residues: 36 loop : -1.69 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.010 0.001 TYR F 51 PHE 0.010 0.001 PHE K 109 TRP 0.009 0.001 TRP K 35 HIS 0.008 0.001 HIS K 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (15264) covalent geometry : angle 0.63277 / 0.35 (21917) hydrogen bonds : bond 0.04585 / 3.19 ( 824) hydrogen bonds : angle 2.84225 / 1.98 ( 2060) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 292 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 95 HIS cc_start: 0.8907 (m90) cc_final: 0.8565 (m90) REVERT: K 96 MET cc_start: 0.8946 (mpp) cc_final: 0.8680 (mpp) REVERT: K 100 GLN cc_start: 0.9177 (tt0) cc_final: 0.8819 (tt0) REVERT: K 245 LYS cc_start: 0.8778 (pttt) cc_final: 0.8189 (ptpp) REVERT: A 73 GLU cc_start: 0.8878 (tt0) cc_final: 0.8511 (tt0) REVERT: A 76 GLN cc_start: 0.9158 (pp30) cc_final: 0.8842 (pp30) REVERT: C 36 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.9010 (mtmm) REVERT: C 99 ARG cc_start: 0.8957 (ptp90) cc_final: 0.8644 (ptp-110) REVERT: D 33 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7553 (mtt-85) REVERT: D 68 ASP cc_start: 0.9032 (t70) cc_final: 0.8505 (t0) REVERT: D 85 LYS cc_start: 0.9459 (mmtm) cc_final: 0.9240 (mmtt) REVERT: E 129 ARG cc_start: 0.9019 (tpp80) cc_final: 0.8687 (tpp80) REVERT: F 25 ASN cc_start: 0.8686 (m-40) cc_final: 0.8420 (m110) REVERT: G 15 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7689 (mtpp) REVERT: G 74 LYS cc_start: 0.9556 (mmtt) cc_final: 0.9238 (mmmm) REVERT: H 87 THR cc_start: 0.9515 (p) cc_final: 0.8646 (t) REVERT: H 90 GLU cc_start: 0.8902 (mp0) cc_final: 0.7716 (mp0) REVERT: H 102 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8352 (mm-30) outliers start: 17 outliers final: 13 residues processed: 299 average time/residue: 0.1263 time to fit residues: 51.2851 Evaluate side-chains 296 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 282 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 12 optimal weight: 4.9990 chunk 67 optimal weight: 0.0570 chunk 125 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 17 optimal weight: 0.0370 chunk 126 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 102 optimal weight: 40.0000 chunk 96 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.094119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.058667 restraints weight = 33368.369| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.11 r_work: 0.2584 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15264 Z= 0.168 Angle : 0.655 15.232 21917 Z= 0.358 Chirality : 0.044 0.317 2508 Planarity : 0.005 0.134 1749 Dihedral : 29.794 176.746 4453 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.36 % Favored : 96.26 % Rotamer: Outliers : 2.26 % Allowed : 16.65 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.27), residues: 1043 helix: 2.11 (0.21), residues: 610 sheet: -1.11 (0.96), residues: 35 loop : -1.65 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 83 TYR 0.010 0.001 TYR F 51 PHE 0.010 0.001 PHE K 124 TRP 0.014 0.002 TRP K 188 HIS 0.007 0.001 HIS K 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (15264) covalent geometry : angle 0.65496 / 0.36 (21917) hydrogen bonds : bond 0.04762 / 3.31 ( 824) hydrogen bonds : angle 2.82506 / 1.98 ( 2060) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 287 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 95 HIS cc_start: 0.8864 (m90) cc_final: 0.8580 (m90) REVERT: K 96 MET cc_start: 0.8875 (mpp) cc_final: 0.8581 (mpp) REVERT: K 100 GLN cc_start: 0.9109 (tt0) cc_final: 0.8769 (tt0) REVERT: K 245 LYS cc_start: 0.8744 (pttt) cc_final: 0.8123 (ptpp) REVERT: A 56 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8805 (ttmt) REVERT: A 73 GLU cc_start: 0.8897 (tt0) cc_final: 0.8626 (tt0) REVERT: B 27 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8865 (mm-40) REVERT: C 36 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8968 (mtmm) REVERT: D 33 ARG cc_start: 0.8326 (mtp85) cc_final: 0.7594 (mtt-85) REVERT: D 68 ASP cc_start: 0.9036 (t70) cc_final: 0.8534 (t0) REVERT: D 85 LYS cc_start: 0.9459 (mmtm) cc_final: 0.9244 (mmtt) REVERT: E 129 ARG cc_start: 0.9031 (tpp80) cc_final: 0.8725 (tpp80) REVERT: F 25 ASN cc_start: 0.8668 (m-40) cc_final: 0.8410 (m110) REVERT: G 15 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7805 (mtpp) REVERT: G 74 LYS cc_start: 0.9515 (mmtt) cc_final: 0.9227 (mmmm) REVERT: H 90 GLU cc_start: 0.8931 (mp0) cc_final: 0.7743 (mp0) REVERT: H 102 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8090 (mm-30) outliers start: 19 outliers final: 13 residues processed: 294 average time/residue: 0.1232 time to fit residues: 49.3942 Evaluate side-chains 295 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 280 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 69 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.059634 restraints weight = 33167.883| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.13 r_work: 0.2614 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15264 Z= 0.133 Angle : 0.637 14.702 21917 Z= 0.350 Chirality : 0.043 0.310 2508 Planarity : 0.005 0.135 1749 Dihedral : 29.767 176.945 4453 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.16 % Favored : 96.45 % Rotamer: Outliers : 1.66 % Allowed : 17.00 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.27), residues: 1043 helix: 2.13 (0.21), residues: 616 sheet: -0.95 (0.97), residues: 35 loop : -1.74 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 83 TYR 0.011 0.001 TYR K 257 PHE 0.007 0.001 PHE K 109 TRP 0.006 0.001 TRP K 276 HIS 0.005 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (15264) covalent geometry : angle 0.63722 / 0.35 (21917) hydrogen bonds : bond 0.04502 / 3.15 ( 824) hydrogen bonds : angle 2.77228 / 1.94 ( 2060) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 292 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 95 HIS cc_start: 0.8920 (m90) cc_final: 0.8647 (m90) REVERT: K 96 MET cc_start: 0.8880 (mpp) cc_final: 0.8551 (mpp) REVERT: K 100 GLN cc_start: 0.9134 (tt0) cc_final: 0.8797 (tt0) REVERT: K 245 LYS cc_start: 0.8720 (pttt) cc_final: 0.8094 (ptpp) REVERT: A 73 GLU cc_start: 0.8913 (tt0) cc_final: 0.8620 (tt0) REVERT: C 36 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8978 (mtmm) REVERT: D 68 ASP cc_start: 0.9043 (t70) cc_final: 0.8537 (t0) REVERT: D 85 LYS cc_start: 0.9463 (mmtm) cc_final: 0.9246 (mmtt) REVERT: E 129 ARG cc_start: 0.9024 (tpp80) cc_final: 0.8713 (tpp80) REVERT: F 25 ASN cc_start: 0.8637 (m-40) cc_final: 0.8372 (m110) REVERT: G 15 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7766 (mtpp) REVERT: G 74 LYS cc_start: 0.9510 (mmtt) cc_final: 0.9221 (mmmm) REVERT: H 90 GLU cc_start: 0.8940 (mp0) cc_final: 0.7718 (mp0) REVERT: H 102 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8142 (mm-30) outliers start: 14 outliers final: 9 residues processed: 298 average time/residue: 0.1325 time to fit residues: 53.4277 Evaluate side-chains 288 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 278 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 50 HIS ** 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 = 0.3528 r_free = 0.3528 target = 0.093711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.058347 restraints weight = 33191.944| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.09 r_work: 0.2580 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15264 Z= 0.177 Angle : 0.660 13.003 21917 Z= 0.360 Chirality : 0.044 0.319 2508 Planarity : 0.005 0.132 1749 Dihedral : 29.851 176.886 4453 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.64 % Favored : 95.97 % Rotamer: Outliers : 2.02 % Allowed : 17.48 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.27), residues: 1043 helix: 2.13 (0.21), residues: 615 sheet: -1.11 (0.94), residues: 36 loop : -1.75 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 8 TYR 0.010 0.001 TYR F 51 PHE 0.017 0.002 PHE K 49 TRP 0.006 0.001 TRP K 35 HIS 0.003 0.001 HIS K 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (15264) covalent geometry : angle 0.66049 / 0.36 (21917) hydrogen bonds : bond 0.04780 / 3.30 ( 824) hydrogen bonds : angle 2.84255 / 2.01 ( 2060) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 283 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 95 HIS cc_start: 0.9009 (m90) cc_final: 0.8732 (m90) REVERT: K 96 MET cc_start: 0.8883 (mpp) cc_final: 0.8575 (mpp) REVERT: K 100 GLN cc_start: 0.9143 (tt0) cc_final: 0.8866 (tt0) REVERT: K 201 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.9008 (p0) REVERT: K 245 LYS cc_start: 0.8644 (pttt) cc_final: 0.8002 (ptpp) REVERT: A 56 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8795 (ttmt) REVERT: A 73 GLU cc_start: 0.8926 (tt0) cc_final: 0.8629 (tt0) REVERT: C 36 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8924 (mtmm) REVERT: D 68 ASP cc_start: 0.9051 (t70) cc_final: 0.8552 (t0) REVERT: D 85 LYS cc_start: 0.9453 (mmtm) cc_final: 0.9238 (mmtt) REVERT: D 93 GLU cc_start: 0.8857 (mp0) cc_final: 0.8507 (mp0) REVERT: F 25 ASN cc_start: 0.8711 (m-40) cc_final: 0.8449 (m110) REVERT: G 15 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7806 (mtmm) REVERT: H 90 GLU cc_start: 0.8956 (mp0) cc_final: 0.7733 (mp0) outliers start: 17 outliers final: 13 residues processed: 290 average time/residue: 0.1249 time to fit residues: 48.7719 Evaluate side-chains 291 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.5980 chunk 131 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 58 optimal weight: 0.0050 chunk 114 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.059165 restraints weight = 33354.584| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.10 r_work: 0.2601 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15264 Z= 0.136 Angle : 0.646 13.767 21917 Z= 0.353 Chirality : 0.043 0.312 2508 Planarity : 0.005 0.130 1749 Dihedral : 29.829 177.129 4453 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.36 % Favored : 96.26 % Rotamer: Outliers : 2.02 % Allowed : 17.95 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 1.01 (0.27), residues: 1043 helix: 2.17 (0.21), residues: 615 sheet: -0.99 (0.97), residues: 36 loop : -1.73 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 83 TYR 0.011 0.001 TYR H 80 PHE 0.007 0.001 PHE A 67 TRP 0.006 0.001 TRP K 276 HIS 0.003 0.000 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (15264) covalent geometry : angle 0.64644 / 0.35 (21917) hydrogen bonds : bond 0.04529 / 3.16 ( 824) hydrogen bonds : angle 2.79306 / 1.96 ( 2060) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 292 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 95 HIS cc_start: 0.8990 (m90) cc_final: 0.8723 (m90) REVERT: K 96 MET cc_start: 0.8874 (mpp) cc_final: 0.8554 (mpp) REVERT: K 100 GLN cc_start: 0.9131 (tt0) cc_final: 0.8795 (tt0) REVERT: K 147 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8591 (mm-40) REVERT: K 197 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9437 (mt) REVERT: K 201 ASP cc_start: 0.9219 (OUTLIER) cc_final: 0.9005 (p0) REVERT: K 245 LYS cc_start: 0.8633 (pttt) cc_final: 0.7990 (ptpp) REVERT: A 56 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8751 (ttmt) REVERT: A 73 GLU cc_start: 0.8932 (tt0) cc_final: 0.8634 (tt0) REVERT: C 36 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8951 (mtmm) REVERT: D 68 ASP cc_start: 0.9040 (t70) cc_final: 0.8545 (t0) REVERT: D 85 LYS cc_start: 0.9460 (mmtm) cc_final: 0.9228 (mmtt) REVERT: D 93 GLU cc_start: 0.8843 (mp0) cc_final: 0.8498 (mp0) REVERT: E 129 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8576 (tpp80) REVERT: G 15 LYS cc_start: 0.8145 (mtpt) cc_final: 0.7798 (mtmm) REVERT: H 90 GLU cc_start: 0.8945 (mp0) cc_final: 0.7726 (mp0) outliers start: 17 outliers final: 12 residues processed: 299 average time/residue: 0.1393 time to fit residues: 56.5970 Evaluate side-chains 299 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 282 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 50 HIS ** 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 = 0.3533 r_free = 0.3533 target = 0.093881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.058591 restraints weight = 33077.329| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.09 r_work: 0.2588 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15264 Z= 0.160 Angle : 0.655 13.031 21917 Z= 0.356 Chirality : 0.044 0.315 2508 Planarity : 0.005 0.127 1749 Dihedral : 29.881 177.054 4453 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.84 % Favored : 95.78 % Rotamer: Outliers : 1.78 % Allowed : 18.79 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 1.02 (0.27), residues: 1043 helix: 2.18 (0.21), residues: 615 sheet: -0.97 (0.97), residues: 36 loop : -1.73 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 83 TYR 0.012 0.001 TYR H 80 PHE 0.025 0.002 PHE K 124 TRP 0.006 0.001 TRP K 188 HIS 0.002 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (15264) covalent geometry : angle 0.65455 / 0.36 (21917) hydrogen bonds : bond 0.04635 / 3.21 ( 824) hydrogen bonds : angle 2.81601 / 1.98 ( 2060) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 285 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 96 MET cc_start: 0.8890 (mpp) cc_final: 0.8567 (mpp) REVERT: K 100 GLN cc_start: 0.9157 (tt0) cc_final: 0.8828 (tt0) REVERT: K 114 ASN cc_start: 0.7639 (m-40) cc_final: 0.7222 (p0) REVERT: K 147 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8619 (mm-40) REVERT: K 201 ASP cc_start: 0.9225 (OUTLIER) cc_final: 0.9018 (p0) REVERT: K 206 ASN cc_start: 0.8750 (m-40) cc_final: 0.8378 (m-40) REVERT: K 219 ILE cc_start: 0.9180 (mm) cc_final: 0.8965 (tp) REVERT: K 245 LYS cc_start: 0.8640 (pttt) cc_final: 0.7985 (ptpp) REVERT: K 255 HIS cc_start: 0.5203 (OUTLIER) cc_final: 0.4953 (m90) REVERT: A 73 GLU cc_start: 0.8940 (tt0) cc_final: 0.8648 (tt0) REVERT: C 36 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8953 (mtmm) REVERT: D 68 ASP cc_start: 0.9051 (t70) cc_final: 0.8555 (t0) REVERT: D 85 LYS cc_start: 0.9456 (mmtm) cc_final: 0.9244 (mmtt) REVERT: D 93 GLU cc_start: 0.8877 (mp0) cc_final: 0.8530 (mp0) REVERT: E 129 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8712 (tpp80) REVERT: G 15 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7803 (mtmm) REVERT: G 89 ASN cc_start: 0.9320 (m-40) cc_final: 0.9006 (m-40) REVERT: H 90 GLU cc_start: 0.8958 (mp0) cc_final: 0.7728 (mp0) outliers start: 15 outliers final: 10 residues processed: 292 average time/residue: 0.1298 time to fit residues: 51.3447 Evaluate side-chains 294 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 280 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 0.0010 chunk 65 optimal weight: 0.0770 chunk 25 optimal weight: 0.0980 chunk 119 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 102 optimal weight: 40.0000 overall best weight: 0.8348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.059282 restraints weight = 33394.140| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.11 r_work: 0.2606 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15264 Z= 0.138 Angle : 0.651 18.164 21917 Z= 0.353 Chirality : 0.043 0.312 2508 Planarity : 0.005 0.088 1749 Dihedral : 29.871 177.379 4453 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.55 % Favored : 96.07 % Rotamer: Outliers : 1.90 % Allowed : 18.31 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.27), residues: 1043 helix: 2.19 (0.21), residues: 615 sheet: -1.06 (0.96), residues: 36 loop : -1.70 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 83 TYR 0.010 0.001 TYR H 80 PHE 0.007 0.001 PHE K 24 TRP 0.006 0.001 TRP K 276 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (15264) covalent geometry : angle 0.65072 / 0.35 (21917) hydrogen bonds : bond 0.04468 / 3.12 ( 824) hydrogen bonds : angle 2.76791 / 1.94 ( 2060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2893.03 seconds wall clock time: 50 minutes 5.04 seconds (3005.04 seconds total)