Starting phenix.real_space_refine on Wed Mar 4 13:49:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g57_29735/03_2026/8g57_29735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g57_29735/03_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_29735/03_2026/8g57_29735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g57_29735/03_2026/8g57_29735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g57_29735/03_2026/8g57_29735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g57_29735/03_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-dev-5986/lib/python3.9/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: 3.16, per 1000 atoms: 0.22 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: 1.10 Conformation dependent library (CDL) restraints added in 454.8 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: 2.19 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: 2.45 Time building geometry restraints manager: 1.48 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=" 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 bond pdb=" CE1 HIS K 246 " pdb=" NE2 HIS K 246 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.63e+01 bond pdb=" C GLU K 202 " pdb=" O GLU K 202 " ideal model delta sigma weight residual 1.237 1.276 -0.040 1.17e-02 7.31e+03 1.15e+01 bond pdb=" C1' DG I 169 " pdb=" N9 DG I 169 " ideal model delta sigma weight residual 1.460 1.397 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1' DA J 1 " pdb=" N9 DA J 1 " ideal model delta sigma weight residual 1.460 1.398 0.062 2.00e-02 2.50e+03 9.61e+00 ... (remaining 15259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21499 2.09 - 4.19: 387 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=" N GLU K 202 " pdb=" CA GLU K 202 " pdb=" C GLU K 202 " ideal model delta sigma weight residual 111.28 106.52 4.76 1.09e+00 8.42e-01 1.91e+01 angle pdb=" C PHE K 24 " pdb=" N ASP K 25 " pdb=" CA ASP K 25 " ideal model delta sigma weight residual 121.80 132.27 -10.47 2.44e+00 1.68e-01 1.84e+01 angle pdb=" N ALA K 207 " pdb=" CA ALA K 207 " pdb=" C ALA K 207 " ideal model delta sigma weight residual 109.96 116.90 -6.94 1.68e+00 3.54e-01 1.71e+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: 2182 0.053 - 0.106: 287 0.106 - 0.158: 34 0.158 - 0.211: 2 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: 1.800 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 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 : 0.004 0.063 15264 Z= 0.204 Angle : 0.646 10.470 21917 Z= 0.402 Chirality : 0.037 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 covalent geometry : bond 0.00387 (15264) covalent geometry : angle 0.64650 (21917) hydrogen bonds : bond 0.11876 ( 824) hydrogen bonds : angle 4.42337 ( 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 : 0.379 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: 0.7924 (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: 0.8368 (mmm) REVERT: F 45 ARG cc_start: 0.8691 (ttt90) cc_final: 0.8446 (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: 0.1609 time to fit residues: 74.9027 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 : 0.375 ------------------------------------------------------------------------------- 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: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN ** K 242 GLN ** 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 = 0.3500 r_free = 0.3500 target = 0.092184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.056668 restraints weight = 33201.978| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.10 r_work: 0.2535 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 15264 Z= 0.291 Angle : 0.645 13.036 21917 Z= 0.367 Chirality : 0.040 0.259 2508 Planarity : 0.006 0.120 1749 Dihedral : 29.549 171.277 4453 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.67 % Allowed : 3.36 % Favored : 95.97 % Rotamer: Outliers : 2.14 % Allowed : 12.01 % Favored : 85.85 % 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: 0.24 (0.27), residues: 1043 helix: 1.51 (0.21), residues: 621 sheet: -2.08 (0.92), residues: 36 loop : -1.95 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 83 TYR 0.017 0.002 TYR F 51 PHE 0.022 0.002 PHE K 109 TRP 0.012 0.001 TRP K 35 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00666 (15264) covalent geometry : angle 0.64550 (21917) hydrogen bonds : bond 0.05303 ( 824) hydrogen bonds : angle 3.16537 ( 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 321 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 303 time to evaluate : 0.355 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: K 93 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8791 (tp40) REVERT: K 95 HIS cc_start: 0.9260 (m90) cc_final: 0.8894 (m90) REVERT: K 96 MET cc_start: 0.8950 (mpp) cc_final: 0.8657 (mpp) REVERT: K 100 GLN cc_start: 0.9205 (tt0) cc_final: 0.8922 (tt0) REVERT: K 124 PHE cc_start: 0.8669 (t80) cc_final: 0.8381 (t80) REVERT: K 128 LYS cc_start: 0.9012 (mmmm) cc_final: 0.8811 (mmmm) REVERT: K 140 GLU cc_start: 0.8686 (tp30) cc_final: 0.8426 (tp30) REVERT: K 246 HIS cc_start: 0.8788 (m90) cc_final: 0.8491 (m90) REVERT: A 73 GLU cc_start: 0.8806 (tt0) cc_final: 0.8401 (tt0) REVERT: A 76 GLN cc_start: 0.9162 (pp30) cc_final: 0.8895 (pp30) REVERT: B 27 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8966 (mm-40) REVERT: B 93 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8718 (mm-40) REVERT: D 68 ASP cc_start: 0.9047 (t70) cc_final: 0.8535 (t0) REVERT: D 85 LYS cc_start: 0.9440 (mmtm) cc_final: 0.9174 (mmtt) REVERT: E 129 ARG cc_start: 0.9009 (tpp80) cc_final: 0.8737 (tpt-90) REVERT: F 67 ARG cc_start: 0.9053 (ttp-110) cc_final: 0.8836 (ttp80) REVERT: G 15 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7922 (mtpp) REVERT: G 74 LYS cc_start: 0.9512 (mmtt) cc_final: 0.9219 (mmmm) REVERT: G 76 THR cc_start: 0.9273 (p) cc_final: 0.9061 (t) REVERT: G 104 GLN cc_start: 0.9032 (mm110) cc_final: 0.8788 (mm110) REVERT: H 102 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8422 (mm-30) outliers start: 18 outliers final: 13 residues processed: 309 average time/residue: 0.1484 time to fit residues: 61.3166 Evaluate side-chains 295 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 282 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 58 THR 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 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: 0.7980 chunk 46 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3517 r_free = 0.3517 target = 0.093177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.057733 restraints weight = 33570.594| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.11 r_work: 0.2565 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15264 Z= 0.198 Angle : 0.603 15.857 21917 Z= 0.341 Chirality : 0.037 0.247 2508 Planarity : 0.005 0.121 1749 Dihedral : 29.557 172.568 4453 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.07 % Favored : 96.36 % Rotamer: Outliers : 1.78 % Allowed : 15.22 % Favored : 83.00 % 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: 0.69 (0.27), residues: 1043 helix: 1.85 (0.21), residues: 613 sheet: -1.67 (0.98), residues: 36 loop : -1.66 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.013 0.001 TYR F 51 PHE 0.008 0.001 PHE C 25 TRP 0.007 0.001 TRP K 276 HIS 0.004 0.001 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00449 (15264) covalent geometry : angle 0.60301 (21917) hydrogen bonds : bond 0.04565 ( 824) hydrogen bonds : angle 2.94688 ( 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 312 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 297 time to evaluate : 0.312 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: K 93 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8795 (tp40) REVERT: K 95 HIS cc_start: 0.9252 (m90) cc_final: 0.8899 (m90) REVERT: K 96 MET cc_start: 0.8879 (mpp) cc_final: 0.8644 (mpp) REVERT: K 100 GLN cc_start: 0.9200 (tt0) cc_final: 0.8842 (tt0) REVERT: K 124 PHE cc_start: 0.8647 (t80) cc_final: 0.8342 (t80) REVERT: K 128 LYS cc_start: 0.9097 (mmmm) cc_final: 0.8755 (mmmm) REVERT: K 147 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8876 (mm-40) REVERT: K 246 HIS cc_start: 0.8743 (m90) cc_final: 0.8254 (m90) REVERT: A 73 GLU cc_start: 0.8853 (tt0) cc_final: 0.8507 (tt0) REVERT: A 76 GLN cc_start: 0.9184 (pp30) cc_final: 0.8945 (pp30) REVERT: B 27 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8925 (mm-40) REVERT: D 68 ASP cc_start: 0.9051 (t70) cc_final: 0.8543 (t0) REVERT: D 85 LYS cc_start: 0.9442 (mmtm) cc_final: 0.9158 (mmtt) REVERT: E 129 ARG cc_start: 0.8992 (tpp80) cc_final: 0.8710 (tpp80) REVERT: G 15 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7673 (mtpp) REVERT: G 76 THR cc_start: 0.9254 (p) cc_final: 0.9043 (t) REVERT: G 104 GLN cc_start: 0.8977 (mm110) cc_final: 0.8747 (mm110) REVERT: H 102 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8012 (mm-30) REVERT: H 105 LYS cc_start: 0.8442 (mtmm) cc_final: 0.8084 (mtmm) outliers start: 15 outliers final: 12 residues processed: 304 average time/residue: 0.1459 time to fit residues: 59.5432 Evaluate side-chains 297 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 285 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 58 THR 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 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: 0.7980 chunk 101 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 120 optimal weight: 4.9990 chunk 1 optimal weight: 0.0870 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 242 GLN ** 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 = 0.094626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.059395 restraints weight = 33331.345| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.12 r_work: 0.2608 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2227 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= 0.152 Angle : 0.574 14.666 21917 Z= 0.324 Chirality : 0.035 0.245 2508 Planarity : 0.005 0.122 1749 Dihedral : 29.520 173.651 4453 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.48 % Allowed : 2.78 % Favored : 96.74 % Rotamer: Outliers : 1.90 % Allowed : 15.58 % Favored : 82.52 % 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: 0.93 (0.27), residues: 1043 helix: 2.07 (0.21), residues: 614 sheet: -1.33 (1.01), residues: 35 loop : -1.65 (0.30), residues: 394 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 0.007 0.001 PHE A 67 TRP 0.008 0.001 TRP K 35 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00339 (15264) covalent geometry : angle 0.57399 (21917) hydrogen bonds : bond 0.04075 ( 824) hydrogen bonds : angle 2.74835 ( 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 316 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 300 time to evaluate : 0.381 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: K 93 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8862 (tp40) REVERT: K 95 HIS cc_start: 0.9256 (m90) cc_final: 0.8971 (m90) REVERT: K 96 MET cc_start: 0.8867 (mpp) cc_final: 0.8627 (mpp) REVERT: K 100 GLN cc_start: 0.9182 (tt0) cc_final: 0.8832 (tt0) REVERT: K 124 PHE cc_start: 0.8675 (t80) cc_final: 0.8401 (t80) REVERT: K 128 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8717 (mmmm) REVERT: K 147 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8726 (mm-40) REVERT: K 246 HIS cc_start: 0.8745 (m90) cc_final: 0.8217 (m90) REVERT: B 27 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8893 (mm-40) REVERT: B 93 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8896 (mm110) REVERT: C 36 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.9005 (mtmm) REVERT: D 68 ASP cc_start: 0.9032 (t70) cc_final: 0.8540 (t0) REVERT: D 85 LYS cc_start: 0.9454 (mmtm) cc_final: 0.9218 (mmtt) REVERT: E 129 ARG cc_start: 0.9007 (tpp80) cc_final: 0.8738 (tpp80) REVERT: G 15 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7718 (mtmm) REVERT: G 72 ASP cc_start: 0.8227 (m-30) cc_final: 0.7992 (m-30) REVERT: G 76 THR cc_start: 0.9230 (p) cc_final: 0.9020 (t) REVERT: G 104 GLN cc_start: 0.9010 (mm110) cc_final: 0.8788 (mm110) REVERT: H 102 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7864 (mm-30) REVERT: H 105 LYS cc_start: 0.8393 (mtmm) cc_final: 0.7988 (mtmm) outliers start: 16 outliers final: 11 residues processed: 307 average time/residue: 0.1508 time to fit residues: 61.9691 Evaluate side-chains 291 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 279 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 36 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.093593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.058188 restraints weight = 33354.644| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.12 r_work: 0.2576 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15264 Z= 0.191 Angle : 0.588 12.494 21917 Z= 0.333 Chirality : 0.036 0.216 2508 Planarity : 0.005 0.103 1749 Dihedral : 29.603 173.178 4453 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.16 % Favored : 96.45 % Rotamer: Outliers : 2.50 % Allowed : 15.70 % Favored : 81.81 % 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: 2.06 (0.21), residues: 618 sheet: -1.49 (0.95), residues: 36 loop : -1.60 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.012 0.001 TYR F 51 PHE 0.008 0.001 PHE C 25 TRP 0.008 0.001 TRP K 35 HIS 0.004 0.001 HIS K 133 Details of bonding type rmsd covalent geometry : bond 0.00435 (15264) covalent geometry : angle 0.58773 (21917) hydrogen bonds : bond 0.04315 ( 824) hydrogen bonds : angle 2.75294 ( 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 317 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 296 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 93 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8876 (tp40) REVERT: K 95 HIS cc_start: 0.9295 (m90) cc_final: 0.8989 (m90) REVERT: K 96 MET cc_start: 0.8897 (mpp) cc_final: 0.8663 (mpp) REVERT: K 100 GLN cc_start: 0.9196 (tt0) cc_final: 0.8842 (tt0) REVERT: K 124 PHE cc_start: 0.8738 (t80) cc_final: 0.8453 (t80) REVERT: K 128 LYS cc_start: 0.9049 (mmmm) cc_final: 0.8783 (mmmm) REVERT: K 147 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8723 (mm-40) REVERT: K 190 ASP cc_start: 0.9100 (m-30) cc_final: 0.8693 (m-30) REVERT: A 56 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8726 (ttmt) REVERT: A 73 GLU cc_start: 0.8934 (tt0) cc_final: 0.8713 (tt0) REVERT: C 36 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9002 (mtmm) REVERT: D 68 ASP cc_start: 0.9057 (t70) cc_final: 0.8556 (t0) REVERT: D 85 LYS cc_start: 0.9456 (mmtm) cc_final: 0.9219 (mmtt) REVERT: E 129 ARG cc_start: 0.9031 (tpp80) cc_final: 0.8737 (tpp80) REVERT: E 133 GLU cc_start: 0.8352 (mp0) cc_final: 0.8140 (mp0) REVERT: G 15 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7777 (mtmm) REVERT: G 104 GLN cc_start: 0.9000 (mm110) cc_final: 0.8768 (mm110) REVERT: H 102 GLU cc_start: 0.8667 (mm-30) cc_final: 0.7902 (mm-30) REVERT: H 105 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8083 (mtmm) outliers start: 21 outliers final: 15 residues processed: 305 average time/residue: 0.1446 time to fit residues: 59.7166 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 : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 197 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 K residue 257 TYR 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 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: 3.9990 chunk 125 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 HIS ** K 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.091249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.056464 restraints weight = 32932.941| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.08 r_work: 0.2532 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15264 Z= 0.266 Angle : 0.633 12.897 21917 Z= 0.357 Chirality : 0.039 0.250 2508 Planarity : 0.005 0.129 1749 Dihedral : 29.768 172.389 4453 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.55 % Favored : 96.07 % Rotamer: Outliers : 2.62 % Allowed : 16.41 % Favored : 80.98 % 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: 0.78 (0.27), residues: 1043 helix: 1.93 (0.21), residues: 626 sheet: -1.49 (0.92), residues: 36 loop : -1.79 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 8 TYR 0.014 0.002 TYR F 51 PHE 0.013 0.001 PHE C 25 TRP 0.011 0.002 TRP K 35 HIS 0.002 0.001 HIS K 255 Details of bonding type rmsd covalent geometry : bond 0.00612 (15264) covalent geometry : angle 0.63285 (21917) hydrogen bonds : bond 0.04892 ( 824) hydrogen bonds : angle 2.90149 ( 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 303 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 281 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 36 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8736 (tm-30) REVERT: K 93 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8774 (tp40) REVERT: K 95 HIS cc_start: 0.9292 (m90) cc_final: 0.8961 (m90) REVERT: K 96 MET cc_start: 0.8865 (mpp) cc_final: 0.8638 (mpp) REVERT: K 100 GLN cc_start: 0.9165 (tt0) cc_final: 0.8888 (tt0) REVERT: K 124 PHE cc_start: 0.8759 (t80) cc_final: 0.8495 (t80) REVERT: K 128 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8855 (mmmm) REVERT: K 147 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8817 (mm-40) REVERT: K 190 ASP cc_start: 0.9077 (m-30) cc_final: 0.8787 (m-30) REVERT: K 224 ASN cc_start: 0.9239 (m110) cc_final: 0.8980 (m110) REVERT: K 257 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.8497 (m-10) REVERT: A 73 GLU cc_start: 0.8975 (tt0) cc_final: 0.8727 (tt0) REVERT: C 36 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8984 (mtmm) REVERT: C 99 ARG cc_start: 0.9096 (ptp-110) cc_final: 0.8879 (ptp-110) REVERT: D 68 ASP cc_start: 0.9087 (t70) cc_final: 0.8585 (t0) REVERT: D 85 LYS cc_start: 0.9463 (mmtm) cc_final: 0.9215 (mmtt) REVERT: E 129 ARG cc_start: 0.9046 (tpp80) cc_final: 0.8713 (tpp80) REVERT: E 133 GLU cc_start: 0.8414 (mp0) cc_final: 0.8156 (mp0) REVERT: F 35 ARG cc_start: 0.8957 (mtp85) cc_final: 0.8666 (mtp85) REVERT: G 15 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7775 (mtmm) REVERT: G 64 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8664 (tm-30) REVERT: G 104 GLN cc_start: 0.9044 (mm110) cc_final: 0.8821 (mm110) REVERT: H 102 GLU cc_start: 0.8749 (mm-30) cc_final: 0.7937 (mm-30) REVERT: H 105 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8175 (mtmm) outliers start: 22 outliers final: 17 residues processed: 289 average time/residue: 0.1565 time to fit residues: 60.8113 Evaluate side-chains 288 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 269 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain K residue 257 TYR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 50 ILE 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 36 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 0.0030 chunk 37 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 242 GLN ** 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 = 0.3520 r_free = 0.3520 target = 0.093008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.057970 restraints weight = 32901.880| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.10 r_work: 0.2571 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15264 Z= 0.145 Angle : 0.602 15.183 21917 Z= 0.340 Chirality : 0.037 0.220 2508 Planarity : 0.005 0.104 1749 Dihedral : 29.750 173.006 4453 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.07 % Favored : 96.55 % Rotamer: Outliers : 2.14 % Allowed : 17.48 % Favored : 80.38 % 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: 2.00 (0.21), residues: 626 sheet: -1.07 (0.90), residues: 41 loop : -1.77 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 29 TYR 0.013 0.001 TYR K 257 PHE 0.007 0.001 PHE K 109 TRP 0.010 0.001 TRP K 35 HIS 0.005 0.001 HIS K 133 Details of bonding type rmsd covalent geometry : bond 0.00316 (15264) covalent geometry : angle 0.60158 (21917) hydrogen bonds : bond 0.04317 ( 824) hydrogen bonds : angle 2.76057 ( 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 310 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 36 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8727 (tm-30) REVERT: K 93 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8819 (tp40) REVERT: K 95 HIS cc_start: 0.9299 (m90) cc_final: 0.8974 (m90) REVERT: K 96 MET cc_start: 0.8835 (mpp) cc_final: 0.8595 (mpp) REVERT: K 100 GLN cc_start: 0.9192 (tt0) cc_final: 0.8908 (tt0) REVERT: K 124 PHE cc_start: 0.8753 (t80) cc_final: 0.8484 (t80) REVERT: K 147 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8669 (mm-40) REVERT: K 190 ASP cc_start: 0.8962 (m-30) cc_final: 0.8716 (m-30) REVERT: K 206 ASN cc_start: 0.8881 (m-40) cc_final: 0.8615 (m-40) REVERT: K 224 ASN cc_start: 0.9225 (m110) cc_final: 0.8921 (m-40) REVERT: K 227 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8923 (mt) REVERT: A 56 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8639 (ttmt) REVERT: A 73 GLU cc_start: 0.8988 (tt0) cc_final: 0.8771 (tt0) REVERT: C 36 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.9003 (mtmm) REVERT: C 99 ARG cc_start: 0.9072 (ptp-110) cc_final: 0.8865 (ptp-110) REVERT: D 68 ASP cc_start: 0.9074 (t70) cc_final: 0.8564 (t0) REVERT: E 129 ARG cc_start: 0.9028 (tpp80) cc_final: 0.8731 (tpp80) REVERT: E 133 GLU cc_start: 0.8374 (mp0) cc_final: 0.8103 (mp0) REVERT: G 15 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7751 (mtmm) REVERT: G 104 GLN cc_start: 0.9046 (mm110) cc_final: 0.8818 (mm110) REVERT: H 102 GLU cc_start: 0.8659 (mm-30) cc_final: 0.7849 (mm-30) REVERT: H 105 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8211 (mtmm) outliers start: 18 outliers final: 13 residues processed: 300 average time/residue: 0.1494 time to fit residues: 60.6110 Evaluate side-chains 296 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 280 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 197 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 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 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: 3.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 242 GLN ** 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 = 0.3539 r_free = 0.3539 target = 0.094001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.058976 restraints weight = 33279.252| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.11 r_work: 0.2606 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2692 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= 0.154 Angle : 0.584 13.905 21917 Z= 0.330 Chirality : 0.036 0.220 2508 Planarity : 0.005 0.106 1749 Dihedral : 29.629 174.181 4453 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.36 % Favored : 96.26 % Rotamer: Outliers : 2.02 % Allowed : 18.07 % Favored : 79.90 % 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: 0.99 (0.27), residues: 1043 helix: 2.09 (0.21), residues: 627 sheet: -0.94 (0.90), residues: 41 loop : -1.77 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 30 TYR 0.009 0.001 TYR C 57 PHE 0.008 0.001 PHE K 109 TRP 0.033 0.002 TRP K 35 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00344 (15264) covalent geometry : angle 0.58448 (21917) hydrogen bonds : bond 0.04001 ( 824) hydrogen bonds : angle 2.68896 ( 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 302 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 285 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 93 GLN cc_start: 0.9074 (tp-100) cc_final: 0.8828 (tp40) REVERT: K 95 HIS cc_start: 0.9237 (m90) cc_final: 0.8991 (m90) REVERT: K 96 MET cc_start: 0.8853 (mpp) cc_final: 0.8631 (mpp) REVERT: K 100 GLN cc_start: 0.9153 (tt0) cc_final: 0.8937 (tt0) REVERT: K 124 PHE cc_start: 0.8652 (t80) cc_final: 0.8366 (t80) REVERT: K 147 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8660 (mm-40) REVERT: K 190 ASP cc_start: 0.8836 (m-30) cc_final: 0.8576 (m-30) REVERT: K 197 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9390 (mt) REVERT: K 206 ASN cc_start: 0.8856 (m-40) cc_final: 0.8578 (m-40) REVERT: K 224 ASN cc_start: 0.9178 (m110) cc_final: 0.8877 (m-40) REVERT: K 227 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8892 (mt) REVERT: K 255 HIS cc_start: 0.4941 (OUTLIER) cc_final: 0.4734 (m90) REVERT: A 73 GLU cc_start: 0.8939 (tt0) cc_final: 0.8722 (tt0) REVERT: C 36 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8925 (mtmm) REVERT: C 99 ARG cc_start: 0.9001 (ptp-110) cc_final: 0.8801 (ptp-110) REVERT: D 68 ASP cc_start: 0.9031 (t70) cc_final: 0.8564 (t0) REVERT: D 93 GLU cc_start: 0.8825 (mp0) cc_final: 0.8579 (mp0) REVERT: E 129 ARG cc_start: 0.9029 (tpp80) cc_final: 0.8812 (tpp80) REVERT: G 15 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7799 (mtmm) REVERT: G 61 GLU cc_start: 0.9005 (tp30) cc_final: 0.8661 (tp30) REVERT: G 89 ASN cc_start: 0.9285 (m-40) cc_final: 0.8942 (m-40) REVERT: G 104 GLN cc_start: 0.9034 (mm110) cc_final: 0.8832 (mm110) REVERT: H 102 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8198 (mm-30) REVERT: H 105 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8173 (mtmm) outliers start: 17 outliers final: 12 residues processed: 294 average time/residue: 0.1458 time to fit residues: 58.3852 Evaluate side-chains 298 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 282 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 197 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 K residue 257 TYR Chi-restraints excluded: chain A residue 58 THR 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: 0.9990 chunk 131 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 0.0010 chunk 114 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 ASN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.057409 restraints weight = 33383.997| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.10 r_work: 0.2565 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15264 Z= 0.204 Angle : 0.608 15.687 21917 Z= 0.342 Chirality : 0.037 0.219 2508 Planarity : 0.005 0.106 1749 Dihedral : 29.714 173.244 4453 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.55 % Favored : 96.07 % Rotamer: Outliers : 2.14 % Allowed : 18.07 % Favored : 79.79 % 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: 0.98 (0.27), residues: 1043 helix: 2.07 (0.21), residues: 625 sheet: -1.07 (0.90), residues: 41 loop : -1.69 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 30 TYR 0.012 0.001 TYR F 51 PHE 0.008 0.001 PHE K 137 TRP 0.007 0.001 TRP K 35 HIS 0.003 0.001 HIS K 119 Details of bonding type rmsd covalent geometry : bond 0.00467 (15264) covalent geometry : angle 0.60776 (21917) hydrogen bonds : bond 0.04409 ( 824) hydrogen bonds : angle 2.80605 ( 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 302 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 284 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 35 TRP cc_start: 0.8834 (m-10) cc_final: 0.8569 (m100) REVERT: K 93 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8778 (tp40) REVERT: K 95 HIS cc_start: 0.9251 (m90) cc_final: 0.8980 (m90) REVERT: K 96 MET cc_start: 0.8877 (mpp) cc_final: 0.8661 (mpp) REVERT: K 100 GLN cc_start: 0.9160 (tt0) cc_final: 0.8881 (tt0) REVERT: K 124 PHE cc_start: 0.8606 (t80) cc_final: 0.8368 (t80) REVERT: K 147 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8770 (mm-40) REVERT: K 190 ASP cc_start: 0.8904 (m-30) cc_final: 0.8636 (m-30) REVERT: K 197 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9425 (mt) REVERT: K 206 ASN cc_start: 0.8888 (m-40) cc_final: 0.8603 (m-40) REVERT: K 224 ASN cc_start: 0.9189 (m110) cc_final: 0.8893 (m-40) REVERT: K 227 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8918 (mt) REVERT: K 255 HIS cc_start: 0.4899 (OUTLIER) cc_final: 0.4695 (m90) REVERT: K 286 LEU cc_start: 0.8752 (mt) cc_final: 0.8526 (pt) REVERT: A 73 GLU cc_start: 0.8943 (tt0) cc_final: 0.8734 (tt0) REVERT: C 36 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8913 (mtmm) REVERT: C 99 ARG cc_start: 0.9012 (ptp-110) cc_final: 0.8800 (ptp-110) REVERT: D 33 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7928 (mtp85) REVERT: D 68 ASP cc_start: 0.9062 (t70) cc_final: 0.8585 (t0) REVERT: D 93 GLU cc_start: 0.8868 (mp0) cc_final: 0.8575 (mp0) REVERT: E 129 ARG cc_start: 0.9045 (tpp80) cc_final: 0.8829 (tpp80) REVERT: F 35 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8647 (mtp85) REVERT: G 15 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7819 (mtmm) REVERT: G 61 GLU cc_start: 0.9058 (tp30) cc_final: 0.8665 (tp30) REVERT: G 64 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8681 (tm-30) REVERT: G 89 ASN cc_start: 0.9330 (m-40) cc_final: 0.8978 (m-40) REVERT: G 104 GLN cc_start: 0.9041 (mm110) cc_final: 0.8821 (mm110) REVERT: H 102 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7780 (mm-30) REVERT: H 105 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8193 (mtmm) outliers start: 18 outliers final: 12 residues processed: 293 average time/residue: 0.1536 time to fit residues: 61.0861 Evaluate side-chains 292 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 276 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 197 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 58 THR 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 Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 23 optimal weight: 0.0000 chunk 94 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 65 optimal weight: 0.0970 chunk 126 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 ASN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.094243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.059266 restraints weight = 33053.210| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.10 r_work: 0.2612 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2799 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= 0.140 Angle : 0.592 15.718 21917 Z= 0.332 Chirality : 0.036 0.222 2508 Planarity : 0.005 0.106 1749 Dihedral : 29.656 173.764 4453 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.74 % Favored : 95.97 % Rotamer: Outliers : 1.78 % Allowed : 18.91 % Favored : 79.31 % 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: 1.14 (0.27), residues: 1043 helix: 2.19 (0.21), residues: 617 sheet: -1.01 (0.91), residues: 41 loop : -1.52 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG A 8 TYR 0.009 0.001 TYR F 51 PHE 0.010 0.001 PHE K 49 TRP 0.006 0.001 TRP K 276 HIS 0.006 0.001 HIS K 119 Details of bonding type rmsd covalent geometry : bond 0.00307 (15264) covalent geometry : angle 0.59202 (21917) hydrogen bonds : bond 0.03997 ( 824) hydrogen bonds : angle 2.71446 ( 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 304 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 289 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 46 ASN cc_start: 0.8568 (t0) cc_final: 0.8123 (t0) REVERT: K 93 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8770 (tp40) REVERT: K 95 HIS cc_start: 0.9271 (m90) cc_final: 0.8998 (m90) REVERT: K 96 MET cc_start: 0.8840 (mpp) cc_final: 0.8593 (mpp) REVERT: K 100 GLN cc_start: 0.9142 (tt0) cc_final: 0.8857 (tt0) REVERT: K 124 PHE cc_start: 0.8559 (t80) cc_final: 0.8312 (t80) REVERT: K 147 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8780 (mm-40) REVERT: K 190 ASP cc_start: 0.8857 (m-30) cc_final: 0.8583 (m-30) REVERT: K 206 ASN cc_start: 0.8984 (m-40) cc_final: 0.8767 (m-40) REVERT: K 224 ASN cc_start: 0.9150 (m110) cc_final: 0.8847 (m-40) REVERT: K 227 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8909 (mt) REVERT: K 245 LYS cc_start: 0.8882 (ptmm) cc_final: 0.8590 (ptpp) REVERT: K 255 HIS cc_start: 0.5162 (OUTLIER) cc_final: 0.4881 (m90) REVERT: K 286 LEU cc_start: 0.8748 (mt) cc_final: 0.8527 (pt) REVERT: A 73 GLU cc_start: 0.8960 (tt0) cc_final: 0.8749 (tt0) REVERT: C 36 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8932 (mtmm) REVERT: D 33 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7463 (mtp85) REVERT: D 68 ASP cc_start: 0.9030 (t70) cc_final: 0.8562 (t0) REVERT: D 93 GLU cc_start: 0.8863 (mp0) cc_final: 0.8572 (mp0) REVERT: G 15 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7768 (mtmm) REVERT: G 61 GLU cc_start: 0.9001 (tp30) cc_final: 0.8627 (tp30) REVERT: G 77 ARG cc_start: 0.8792 (mtt-85) cc_final: 0.8556 (mtt-85) REVERT: G 104 GLN cc_start: 0.9026 (mm110) cc_final: 0.8819 (mm110) REVERT: H 102 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7709 (mm-30) REVERT: H 105 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8064 (mtmm) outliers start: 15 outliers final: 12 residues processed: 296 average time/residue: 0.1516 time to fit residues: 60.9279 Evaluate side-chains 298 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 283 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 129 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 58 THR 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 Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 HIS ** 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 = 0.3537 r_free = 0.3537 target = 0.093791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.059088 restraints weight = 33394.615| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.09 r_work: 0.2600 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15264 Z= 0.165 Angle : 0.590 15.200 21917 Z= 0.332 Chirality : 0.036 0.216 2508 Planarity : 0.005 0.101 1749 Dihedral : 29.639 173.849 4453 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.74 % Favored : 95.97 % Rotamer: Outliers : 2.02 % Allowed : 18.31 % Favored : 79.67 % 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: 1.16 (0.27), residues: 1043 helix: 2.18 (0.21), residues: 617 sheet: -0.96 (0.90), residues: 41 loop : -1.48 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 30 TYR 0.010 0.001 TYR H 80 PHE 0.006 0.001 PHE A 67 TRP 0.005 0.001 TRP K 276 HIS 0.002 0.001 HIS K 119 Details of bonding type rmsd covalent geometry : bond 0.00373 (15264) covalent geometry : angle 0.59002 (21917) hydrogen bonds : bond 0.04062 ( 824) hydrogen bonds : angle 2.73452 ( 2060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3690.14 seconds wall clock time: 63 minutes 32.65 seconds (3812.65 seconds total)