Starting phenix.real_space_refine on Sat Sep 12 04:46:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k78_22696/09_2026/7k78_22696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k78_22696/09_2026/7k78_22696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k78_22696/09_2026/7k78_22696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k78_22696/09_2026/7k78_22696.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k78_22696/09_2026/7k78_22696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k78_22696/09_2026/7k78_22696.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 232 5.49 5 S 27 5.16 5 C 8210 2.51 5 N 2472 2.21 5 O 3184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14125 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 771 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 802 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} 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: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 722 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2397 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Chain: "J" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2359 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Chain: "K" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1779 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1766 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 3.28, per 1000 atoms: 0.23 Number of scatterers: 14125 At special positions: 0 Unit cell: (116.6, 145.22, 115.54, 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 27 16.00 P 232 15.00 O 3184 8.00 N 2472 7.00 C 8210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS K 44 " - pdb=" SG CYS K 118 " distance=2.03 Simple disulfide: pdb=" SG CYS K 181 " - pdb=" SG CYS K 246 " distance=2.04 Simple disulfide: pdb=" SG CYS L 44 " - pdb=" SG CYS L 118 " distance=2.03 Simple disulfide: pdb=" SG CYS L 181 " - pdb=" SG CYS L 246 " distance=2.03 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: 1.15 Conformation dependent library (CDL) restraints added in 519.5 milliseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 22 sheets defined 46.7% alpha, 21.8% beta 68 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 134 through 148 removed outlier: 4.177A pdb=" N LEU A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 removed outlier: 3.690A pdb=" N PHE A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 208 Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.735A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.706A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 24 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 47 through 75 removed outlier: 4.456A pdb=" N VAL C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 removed outlier: 3.551A pdb=" N LEU C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'D' and resid 41 through 53 removed outlier: 3.745A pdb=" N LYS D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 88 removed outlier: 3.512A pdb=" N ASN D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.536A pdb=" N ILE D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 129 removed outlier: 3.780A pdb=" N LYS D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 148 removed outlier: 3.539A pdb=" N SER E 148 " --> pdb=" O LYS E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 168 removed outlier: 3.649A pdb=" N PHE E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 208 Processing helix chain 'E' and resid 214 through 225 removed outlier: 3.685A pdb=" N MET E 218 " --> pdb=" O MET E 214 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.753A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA F 77 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.640A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL F 88 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 28 through 38 removed outlier: 3.584A pdb=" N VAL G 32 " --> pdb=" O PRO G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 75 removed outlier: 3.540A pdb=" N ASN G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 91 Processing helix chain 'H' and resid 41 through 53 removed outlier: 3.629A pdb=" N LYS H 47 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN H 51 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 88 Processing helix chain 'H' and resid 94 through 106 Processing helix chain 'H' and resid 108 through 129 removed outlier: 3.513A pdb=" N ALA H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 109 through 113 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 84 through 87 Processing helix chain 'L' and resid 109 through 113 removed outlier: 3.562A pdb=" N SER L 113 " --> pdb=" O SER L 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.944A pdb=" N ARG A 177 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 213 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 44 through 45 removed outlier: 7.186A pdb=" N ARG C 44 " --> pdb=" O ILE D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 104 Processing sheet with id=AA7, first strand: chain 'E' and resid 177 through 178 removed outlier: 7.145A pdb=" N ARG E 177 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 Processing sheet with id=AA9, first strand: chain 'G' and resid 44 through 45 removed outlier: 7.184A pdb=" N ARG G 44 " --> pdb=" O ILE H 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 79 through 80 Processing sheet with id=AB2, first strand: chain 'K' and resid 25 through 27 Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.773A pdb=" N THR K 139 " --> pdb=" O GLU K 32 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N TYR K 54 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR K 74 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE K 56 " --> pdb=" O TYR K 72 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR K 72 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TRP K 58 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.773A pdb=" N THR K 139 " --> pdb=" O GLU K 32 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR K 131 " --> pdb=" O ARG K 120 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N SER K 122 " --> pdb=" O LEU K 129 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU K 129 " --> pdb=" O SER K 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 162 through 164 removed outlier: 3.602A pdb=" N PHE K 229 " --> pdb=" O CYS K 181 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN K 227 " --> pdb=" O ALA K 183 " (cutoff:3.500A) removed outlier: 10.630A pdb=" N GLN K 185 " --> pdb=" O SER K 225 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N SER K 225 " --> pdb=" O GLN K 185 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N ILE K 187 " --> pdb=" O SER K 223 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N SER K 223 " --> pdb=" O ILE K 187 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 168 through 170 removed outlier: 6.017A pdb=" N MET K 169 " --> pdb=" O GLU K 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'K' and resid 211 through 212 removed outlier: 6.565A pdb=" N TRP K 193 " --> pdb=" O LEU K 205 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR K 255 " --> pdb=" O GLN K 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 25 through 28 removed outlier: 3.560A pdb=" N THR L 100 " --> pdb=" O ASP L 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 32 through 34 removed outlier: 3.566A pdb=" N VAL L 34 " --> pdb=" O THR L 139 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N TYR L 54 " --> pdb=" O TYR L 74 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR L 74 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE L 56 " --> pdb=" O TYR L 72 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR L 72 " --> pdb=" O ILE L 56 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TRP L 58 " --> pdb=" O ILE L 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 32 through 34 removed outlier: 3.566A pdb=" N VAL L 34 " --> pdb=" O THR L 139 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR L 131 " --> pdb=" O ARG L 120 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N SER L 122 " --> pdb=" O LEU L 129 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU L 129 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 162 through 164 removed outlier: 3.850A pdb=" N ASP L 228 " --> pdb=" O SER L 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 168 through 171 removed outlier: 3.849A pdb=" N ALA L 242 " --> pdb=" O LEU L 262 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU L 191 " --> pdb=" O TYR L 207 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR L 207 " --> pdb=" O LEU L 191 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TRP L 193 " --> pdb=" O LEU L 205 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 168 through 171 removed outlier: 3.849A pdb=" N ALA L 242 " --> pdb=" O LEU L 262 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN L 248 " --> pdb=" O THR L 255 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR L 255 " --> pdb=" O GLN L 248 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3489 1.34 - 1.46: 4289 1.46 - 1.58: 6578 1.58 - 1.70: 462 1.70 - 1.82: 46 Bond restraints: 14864 Sorted by residual: bond pdb=" C3' DT I 38 " pdb=" C2' DT I 38 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.32e+01 bond pdb=" C3' DT I 117 " pdb=" C2' DT I 117 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DT J 215 " pdb=" C2' DT J 215 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DT I 68 " pdb=" C2' DT I 68 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DT J 203 " pdb=" C2' DT J 203 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 ... (remaining 14859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 19439 1.56 - 3.12: 1571 3.12 - 4.67: 74 4.67 - 6.23: 11 6.23 - 7.79: 4 Bond angle restraints: 21099 Sorted by residual: angle pdb=" O4' DA J 273 " pdb=" C4' DA J 273 " pdb=" C3' DA J 273 " ideal model delta sigma weight residual 106.00 102.25 3.75 6.00e-01 2.78e+00 3.91e+01 angle pdb=" O4' DA J 272 " pdb=" C4' DA J 272 " pdb=" C3' DA J 272 " ideal model delta sigma weight residual 106.00 102.44 3.56 6.00e-01 2.78e+00 3.51e+01 angle pdb=" N ASP A 173 " pdb=" CA ASP A 173 " pdb=" C ASP A 173 " ideal model delta sigma weight residual 114.56 107.21 7.35 1.27e+00 6.20e-01 3.35e+01 angle pdb=" O4' DA I 105 " pdb=" C4' DA I 105 " pdb=" C3' DA I 105 " ideal model delta sigma weight residual 106.00 103.06 2.94 6.00e-01 2.78e+00 2.40e+01 angle pdb=" O4' DC J 233 " pdb=" C4' DC J 233 " pdb=" C3' DC J 233 " ideal model delta sigma weight residual 106.00 103.13 2.87 6.00e-01 2.78e+00 2.29e+01 ... (remaining 21094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 6931 32.09 - 64.18: 1537 64.18 - 96.26: 54 96.26 - 128.35: 0 128.35 - 160.44: 2 Dihedral angle restraints: 8524 sinusoidal: 5037 harmonic: 3487 Sorted by residual: dihedral pdb=" CB CYS K 181 " pdb=" SG CYS K 181 " pdb=" SG CYS K 246 " pdb=" CB CYS K 246 " ideal model delta sinusoidal sigma weight residual -86.00 -8.78 -77.22 1 1.00e+01 1.00e-02 7.48e+01 dihedral pdb=" CB CYS L 181 " pdb=" SG CYS L 181 " pdb=" SG CYS L 246 " pdb=" CB CYS L 246 " ideal model delta sinusoidal sigma weight residual 93.00 29.98 63.02 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" C4' DA J 225 " pdb=" C3' DA J 225 " pdb=" O3' DA J 225 " pdb=" P DT J 226 " ideal model delta sinusoidal sigma weight residual 220.00 59.56 160.44 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 8521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1586 0.038 - 0.075: 602 0.075 - 0.113: 167 0.113 - 0.151: 36 0.151 - 0.189: 5 Chirality restraints: 2396 Sorted by residual: chirality pdb=" C3' DT J 236 " pdb=" C4' DT J 236 " pdb=" O3' DT J 236 " pdb=" C2' DT J 236 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" C3' DT I 94 " pdb=" C4' DT I 94 " pdb=" O3' DT I 94 " pdb=" C2' DT I 94 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" C3' DA J 225 " pdb=" C4' DA J 225 " pdb=" O3' DA J 225 " pdb=" C2' DA J 225 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 2393 not shown) Planarity restraints: 1855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET K 42 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO K 43 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO K 43 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO K 43 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS H 53 " 0.033 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO H 54 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 54 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 54 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 272 " -0.023 2.00e-02 2.50e+03 1.19e-02 3.89e+00 pdb=" N9 DA J 272 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA J 272 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DA J 272 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA J 272 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA J 272 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA J 272 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DA J 272 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DA J 272 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA J 272 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA J 272 " -0.006 2.00e-02 2.50e+03 ... (remaining 1852 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 640 2.70 - 3.25: 12284 3.25 - 3.80: 24033 3.80 - 4.35: 32266 4.35 - 4.90: 49096 Nonbonded interactions: 118319 Sorted by model distance: nonbonded pdb=" O ASN C 101 " pdb=" ND2 ASN C 101 " model vdw 2.149 3.120 nonbonded pdb=" OE1 GLN K 61 " pdb=" OH TYR K 117 " model vdw 2.158 3.040 nonbonded pdb=" OD2 ASP L 95 " pdb=" OG SER L 98 " model vdw 2.181 3.040 nonbonded pdb=" OH TYR C 52 " pdb=" OE1 GLN D 99 " model vdw 2.217 3.040 nonbonded pdb=" OE1 GLN L 61 " pdb=" OH TYR L 117 " model vdw 2.223 3.040 ... (remaining 118314 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 134 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 228)) selection = (chain 'E' and resid 134 through 228) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 103) } ncs_group { reference = (chain 'C' and (resid 16 through 72 or (resid 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 115)) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 37 or (resid 38 and (name N or name CA or name C or name O \ or name CB )) or resid 39 through 129)) selection = chain 'H' } ncs_group { reference = (chain 'K' and (resid 23 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 86 or (resid 87 and (name N or nam \ e CA or name C or name O or name CB )) or resid 88 or (resid 89 through 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 157 or ( \ resid 158 and (name N or name CA or name C or name O or name CB )) or resid 159 \ through 265)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.180 Find NCS groups from input model: 0.190 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14868 Z= 0.458 Angle : 0.825 7.791 21107 Z= 0.699 Chirality : 0.044 0.189 2396 Planarity : 0.005 0.058 1855 Dihedral : 27.106 160.440 6276 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.20 % Allowed : 0.99 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1174 helix: 1.41 (0.23), residues: 522 sheet: 0.39 (0.33), residues: 238 loop : -1.62 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 79 TYR 0.022 0.002 TYR L 117 PHE 0.014 0.002 PHE A 169 TRP 0.018 0.002 TRP K 132 HIS 0.006 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.46 (14864) covalent geometry : angle 0.82059 / 0.70 (21099) SS BOND : bond 0.00466 / 0.33 ( 4) SS BOND : angle 4.42212 / 2.97 ( 8) hydrogen bonds : bond 0.18738 / 12.39 ( 661) hydrogen bonds : angle 6.56541 / 4.52 ( 1776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 0.428 Fit side-chains REVERT: A 174 GLN cc_start: 0.7283 (tt0) cc_final: 0.7060 (tt0) REVERT: B 75 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7377 (mt-10) REVERT: E 177 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8256 (mtp85) REVERT: F 80 LYS cc_start: 0.8424 (mttm) cc_final: 0.8119 (mttt) REVERT: K 188 ARG cc_start: 0.7516 (mtm180) cc_final: 0.7113 (mtm110) REVERT: K 251 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7036 (mp0) REVERT: L 65 GLN cc_start: 0.7690 (mp10) cc_final: 0.7270 (mp10) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.1717 time to fit residues: 38.8802 Evaluate side-chains 158 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN H 67 ASN K 170 HIS K 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.166024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116812 restraints weight = 16044.408| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.30 r_work: 0.2993 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14868 Z= 0.184 Angle : 0.702 7.580 21107 Z= 0.396 Chirality : 0.047 0.279 2396 Planarity : 0.005 0.057 1855 Dihedral : 29.639 161.752 4056 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.69 % Allowed : 9.18 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1174 helix: 2.15 (0.22), residues: 528 sheet: 0.81 (0.33), residues: 236 loop : -1.56 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 219 TYR 0.013 0.002 TYR G 52 PHE 0.010 0.001 PHE A 169 TRP 0.011 0.001 TRP K 132 HIS 0.005 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (14864) covalent geometry : angle 0.70118 / 0.40 (21099) SS BOND : bond 0.00505 / 0.31 ( 4) SS BOND : angle 2.15228 / 1.25 ( 8) hydrogen bonds : bond 0.06419 / 4.45 ( 661) hydrogen bonds : angle 3.99080 / 2.80 ( 1776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: E 177 ARG cc_start: 0.8927 (mtp85) cc_final: 0.8602 (mtp85) REVERT: K 84 GLU cc_start: 0.8335 (tp30) cc_final: 0.8105 (mm-30) REVERT: K 160 ILE cc_start: 0.8771 (mt) cc_final: 0.8375 (mp) REVERT: K 219 ARG cc_start: 0.8415 (mtp180) cc_final: 0.8207 (mtm110) REVERT: K 251 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7467 (mp0) REVERT: L 32 GLU cc_start: 0.6429 (mt-10) cc_final: 0.6059 (mt-10) REVERT: L 65 GLN cc_start: 0.7983 (mp10) cc_final: 0.7406 (mp10) outliers start: 7 outliers final: 4 residues processed: 160 average time/residue: 0.1682 time to fit residues: 36.1952 Evaluate side-chains 158 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 261 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 104 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN G 86 GLN K 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.115091 restraints weight = 16132.855| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.32 r_work: 0.2969 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14868 Z= 0.217 Angle : 0.674 6.885 21107 Z= 0.382 Chirality : 0.045 0.294 2396 Planarity : 0.005 0.046 1855 Dihedral : 29.551 161.123 4056 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.38 % Allowed : 13.13 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.24), residues: 1174 helix: 2.28 (0.22), residues: 529 sheet: 0.86 (0.33), residues: 236 loop : -1.63 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 79 TYR 0.013 0.002 TYR D 125 PHE 0.012 0.002 PHE A 169 TRP 0.012 0.002 TRP K 132 HIS 0.006 0.001 HIS L 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (14864) covalent geometry : angle 0.67197 / 0.38 (21099) SS BOND : bond 0.00585 / 0.40 ( 4) SS BOND : angle 2.85950 / 2.06 ( 8) hydrogen bonds : bond 0.06372 / 4.36 ( 661) hydrogen bonds : angle 3.79917 / 2.66 ( 1776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.525 Fit side-chains REVERT: G 64 ILE cc_start: 0.8894 (mm) cc_final: 0.8679 (mm) REVERT: K 84 GLU cc_start: 0.8338 (tp30) cc_final: 0.8131 (mm-30) REVERT: K 251 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7497 (mp0) REVERT: L 65 GLN cc_start: 0.7993 (mp10) cc_final: 0.7425 (mp10) REVERT: L 68 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7737 (mm-30) outliers start: 14 outliers final: 10 residues processed: 159 average time/residue: 0.1640 time to fit residues: 35.6855 Evaluate side-chains 157 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 170 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 106 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN G 86 GLN K 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.171347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118672 restraints weight = 15771.241| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.13 r_work: 0.2985 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14868 Z= 0.144 Angle : 0.606 6.490 21107 Z= 0.349 Chirality : 0.041 0.284 2396 Planarity : 0.004 0.050 1855 Dihedral : 29.334 164.084 4056 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.17 % Allowed : 14.22 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.47 (0.25), residues: 1174 helix: 2.65 (0.22), residues: 529 sheet: 0.99 (0.33), residues: 236 loop : -1.40 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 79 TYR 0.009 0.001 TYR A 145 PHE 0.006 0.001 PHE E 158 TRP 0.008 0.001 TRP K 132 HIS 0.003 0.001 HIS L 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (14864) covalent geometry : angle 0.60556 / 0.35 (21099) SS BOND : bond 0.00612 / 0.31 ( 4) SS BOND : angle 1.25655 / 0.65 ( 8) hydrogen bonds : bond 0.05216 / 3.58 ( 661) hydrogen bonds : angle 3.52805 / 2.47 ( 1776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.425 Fit side-chains REVERT: A 174 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6607 (tt0) REVERT: B 75 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7989 (mt-10) REVERT: F 80 LYS cc_start: 0.8850 (mttm) cc_final: 0.8560 (mttt) REVERT: F 94 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8626 (mp10) REVERT: K 84 GLU cc_start: 0.8492 (tp30) cc_final: 0.8276 (mm-30) REVERT: K 130 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7924 (p0) REVERT: K 160 ILE cc_start: 0.8684 (mt) cc_final: 0.8461 (mp) REVERT: K 214 ASP cc_start: 0.7662 (m-30) cc_final: 0.7354 (p0) REVERT: K 251 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7529 (mp0) REVERT: L 65 GLN cc_start: 0.7899 (mp10) cc_final: 0.7334 (mp10) REVERT: L 237 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6982 (mt-10) outliers start: 22 outliers final: 14 residues processed: 166 average time/residue: 0.1545 time to fit residues: 35.0390 Evaluate side-chains 163 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 170 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 88 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 85 optimal weight: 30.0000 chunk 130 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN G 86 GLN K 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.166849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119603 restraints weight = 16164.409| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.26 r_work: 0.2876 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14868 Z= 0.246 Angle : 0.672 6.409 21107 Z= 0.377 Chirality : 0.045 0.311 2396 Planarity : 0.005 0.057 1855 Dihedral : 29.420 161.756 4056 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.17 % Allowed : 16.19 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.24), residues: 1174 helix: 2.38 (0.22), residues: 529 sheet: 0.91 (0.33), residues: 236 loop : -1.57 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 79 TYR 0.014 0.002 TYR K 117 PHE 0.014 0.002 PHE A 169 TRP 0.011 0.002 TRP K 132 HIS 0.007 0.002 HIS L 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.25 (14864) covalent geometry : angle 0.67106 / 0.38 (21099) SS BOND : bond 0.00634 / 0.34 ( 4) SS BOND : angle 1.88696 / 0.95 ( 8) hydrogen bonds : bond 0.06282 / 4.30 ( 661) hydrogen bonds : angle 3.64237 / 2.54 ( 1776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.415 Fit side-chains REVERT: B 75 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8185 (mt-10) REVERT: K 251 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7648 (mp0) REVERT: L 65 GLN cc_start: 0.8039 (mp10) cc_final: 0.7506 (mp10) REVERT: L 68 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7994 (mm-30) outliers start: 22 outliers final: 19 residues processed: 161 average time/residue: 0.1569 time to fit residues: 34.1964 Evaluate side-chains 167 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 170 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 83 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 30.0000 chunk 98 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 116 optimal weight: 30.0000 chunk 130 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN G 86 GLN K 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.170389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.117195 restraints weight = 15642.994| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.14 r_work: 0.2974 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14868 Z= 0.136 Angle : 0.603 6.235 21107 Z= 0.345 Chirality : 0.041 0.298 2396 Planarity : 0.004 0.052 1855 Dihedral : 29.309 164.615 4056 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.37 % Allowed : 16.98 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.25), residues: 1174 helix: 2.78 (0.22), residues: 529 sheet: 0.93 (0.33), residues: 236 loop : -1.36 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 126 TYR 0.011 0.001 TYR K 117 PHE 0.009 0.001 PHE A 169 TRP 0.008 0.001 TRP K 132 HIS 0.003 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (14864) covalent geometry : angle 0.60267 / 0.35 (21099) SS BOND : bond 0.00529 / 0.28 ( 4) SS BOND : angle 1.66195 / 0.71 ( 8) hydrogen bonds : bond 0.05132 / 3.53 ( 661) hydrogen bonds : angle 3.43593 / 2.40 ( 1776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.342 Fit side-chains REVERT: A 174 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6437 (pm20) REVERT: D 75 GLU cc_start: 0.8290 (pp20) cc_final: 0.7993 (pt0) REVERT: F 80 LYS cc_start: 0.8880 (mttm) cc_final: 0.8558 (mttt) REVERT: F 94 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8639 (mp10) REVERT: H 67 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8790 (m-40) REVERT: K 158 MET cc_start: 0.6641 (mmm) cc_final: 0.6427 (mmp) REVERT: K 214 ASP cc_start: 0.7609 (m-30) cc_final: 0.7324 (p0) REVERT: K 251 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7530 (mp0) REVERT: L 65 GLN cc_start: 0.7848 (mp10) cc_final: 0.7297 (mp10) outliers start: 24 outliers final: 19 residues processed: 168 average time/residue: 0.1566 time to fit residues: 35.6689 Evaluate side-chains 172 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 170 HIS Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 117 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 88 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN G 86 GLN K 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.170343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117004 restraints weight = 15742.904| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.16 r_work: 0.2969 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14868 Z= 0.152 Angle : 0.593 6.455 21107 Z= 0.341 Chirality : 0.040 0.312 2396 Planarity : 0.004 0.049 1855 Dihedral : 29.195 165.299 4056 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.86 % Allowed : 16.78 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.25), residues: 1174 helix: 2.83 (0.22), residues: 530 sheet: 0.95 (0.34), residues: 236 loop : -1.32 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 79 TYR 0.013 0.001 TYR A 145 PHE 0.008 0.001 PHE A 158 TRP 0.007 0.001 TRP K 132 HIS 0.004 0.001 HIS L 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (14864) covalent geometry : angle 0.59242 / 0.34 (21099) SS BOND : bond 0.00435 / 0.24 ( 4) SS BOND : angle 1.31035 / 0.65 ( 8) hydrogen bonds : bond 0.05098 / 3.48 ( 661) hydrogen bonds : angle 3.36436 / 2.35 ( 1776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.446 Fit side-chains REVERT: D 75 GLU cc_start: 0.8334 (pp20) cc_final: 0.8022 (pt0) REVERT: F 80 LYS cc_start: 0.8851 (mttm) cc_final: 0.8519 (mttt) REVERT: F 94 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8635 (mp10) REVERT: H 67 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8790 (m-40) REVERT: K 214 ASP cc_start: 0.7560 (m-30) cc_final: 0.7309 (p0) REVERT: K 251 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7479 (mp0) REVERT: L 65 GLN cc_start: 0.7886 (mp10) cc_final: 0.7338 (mp10) outliers start: 29 outliers final: 22 residues processed: 168 average time/residue: 0.1686 time to fit residues: 37.9821 Evaluate side-chains 173 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 170 HIS Chi-restraints excluded: chain L residue 173 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN G 86 GLN K 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.171157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.117147 restraints weight = 15732.857| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.14 r_work: 0.2986 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14868 Z= 0.133 Angle : 0.577 8.035 21107 Z= 0.333 Chirality : 0.040 0.308 2396 Planarity : 0.004 0.046 1855 Dihedral : 29.147 166.876 4056 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.47 % Allowed : 17.18 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.25), residues: 1174 helix: 2.96 (0.22), residues: 530 sheet: 0.95 (0.34), residues: 236 loop : -1.24 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 126 TYR 0.016 0.001 TYR H 46 PHE 0.008 0.001 PHE A 169 TRP 0.007 0.001 TRP K 132 HIS 0.003 0.001 HIS K 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (14864) covalent geometry : angle 0.57650 / 0.33 (21099) SS BOND : bond 0.00199 / 0.12 ( 4) SS BOND : angle 1.80952 / 0.77 ( 8) hydrogen bonds : bond 0.04791 / 3.28 ( 661) hydrogen bonds : angle 3.30021 / 2.30 ( 1776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.364 Fit side-chains REVERT: D 75 GLU cc_start: 0.8291 (pp20) cc_final: 0.7981 (pt0) REVERT: F 80 LYS cc_start: 0.8855 (mttm) cc_final: 0.8520 (mttt) REVERT: F 94 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8634 (mp10) REVERT: K 158 MET cc_start: 0.6752 (mmm) cc_final: 0.6546 (mmp) REVERT: K 206 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9047 (mt) REVERT: K 214 ASP cc_start: 0.7633 (m-30) cc_final: 0.7309 (p0) REVERT: K 251 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7401 (mp0) REVERT: L 65 GLN cc_start: 0.7869 (mp10) cc_final: 0.7334 (mp10) REVERT: L 162 MET cc_start: 0.8458 (mmm) cc_final: 0.7249 (mmm) outliers start: 25 outliers final: 20 residues processed: 165 average time/residue: 0.1548 time to fit residues: 34.6740 Evaluate side-chains 166 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 206 ILE Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 170 HIS Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 132 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 85 optimal weight: 30.0000 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN G 86 GLN K 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.171975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.118273 restraints weight = 15711.569| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.13 r_work: 0.2982 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14868 Z= 0.148 Angle : 0.587 8.283 21107 Z= 0.337 Chirality : 0.040 0.321 2396 Planarity : 0.004 0.043 1855 Dihedral : 29.091 168.873 4056 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.86 % Allowed : 16.98 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.25), residues: 1174 helix: 2.91 (0.22), residues: 530 sheet: 0.95 (0.34), residues: 236 loop : -1.24 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 126 TYR 0.013 0.001 TYR A 145 PHE 0.007 0.001 PHE A 158 TRP 0.008 0.001 TRP L 193 HIS 0.004 0.001 HIS L 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (14864) covalent geometry : angle 0.58567 / 0.34 (21099) SS BOND : bond 0.00521 / 0.27 ( 4) SS BOND : angle 2.17800 / 0.94 ( 8) hydrogen bonds : bond 0.04928 / 3.36 ( 661) hydrogen bonds : angle 3.28771 / 2.29 ( 1776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: D 75 GLU cc_start: 0.8286 (pp20) cc_final: 0.7978 (pt0) REVERT: F 80 LYS cc_start: 0.8869 (mttm) cc_final: 0.8537 (mttt) REVERT: F 94 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8622 (mp10) REVERT: K 158 MET cc_start: 0.6741 (mmm) cc_final: 0.6534 (mmp) REVERT: K 206 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9077 (mt) REVERT: K 214 ASP cc_start: 0.7589 (m-30) cc_final: 0.7303 (p0) REVERT: K 251 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7411 (mp0) REVERT: K 261 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7483 (tttp) REVERT: L 65 GLN cc_start: 0.7887 (mp10) cc_final: 0.7353 (mp10) REVERT: L 173 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8124 (tt) outliers start: 29 outliers final: 20 residues processed: 167 average time/residue: 0.1584 time to fit residues: 35.9958 Evaluate side-chains 172 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 206 ILE Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 170 HIS Chi-restraints excluded: chain L residue 173 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 132 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 121 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 82 optimal weight: 40.0000 chunk 11 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 114 optimal weight: 0.5980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN K 170 HIS L 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.172636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119348 restraints weight = 15727.431| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.13 r_work: 0.2991 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14868 Z= 0.140 Angle : 0.582 8.187 21107 Z= 0.335 Chirality : 0.039 0.321 2396 Planarity : 0.004 0.043 1855 Dihedral : 29.078 169.568 4056 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.37 % Allowed : 17.28 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.77 (0.25), residues: 1174 helix: 2.96 (0.22), residues: 530 sheet: 0.93 (0.34), residues: 236 loop : -1.22 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 126 TYR 0.010 0.001 TYR A 145 PHE 0.006 0.001 PHE A 169 TRP 0.007 0.001 TRP K 132 HIS 0.005 0.001 HIS L 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (14864) covalent geometry : angle 0.57801 / 0.33 (21099) SS BOND : bond 0.00252 / 0.14 ( 4) SS BOND : angle 3.60948 / 1.41 ( 8) hydrogen bonds : bond 0.04811 / 3.28 ( 661) hydrogen bonds : angle 3.27628 / 2.28 ( 1776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.415 Fit side-chains REVERT: D 75 GLU cc_start: 0.8286 (pp20) cc_final: 0.7978 (pt0) REVERT: F 80 LYS cc_start: 0.8873 (mttm) cc_final: 0.8544 (mttt) REVERT: F 94 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8622 (mp10) REVERT: K 206 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9073 (mt) REVERT: K 214 ASP cc_start: 0.7627 (m-30) cc_final: 0.7309 (p0) REVERT: K 251 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7409 (mp0) REVERT: K 261 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7478 (tttp) REVERT: L 65 GLN cc_start: 0.7899 (mp10) cc_final: 0.7358 (mp10) REVERT: L 173 LEU cc_start: 0.8389 (mt) cc_final: 0.8129 (tt) outliers start: 24 outliers final: 21 residues processed: 160 average time/residue: 0.1550 time to fit residues: 33.9873 Evaluate side-chains 166 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 206 ILE Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 160 ILE Chi-restraints excluded: chain L residue 170 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 131 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 chunk 82 optimal weight: 40.0000 chunk 87 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 86 GLN K 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.172270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118522 restraints weight = 15708.016| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.13 r_work: 0.2986 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 14868 Z= 0.194 Angle : 0.796 59.195 21107 Z= 0.476 Chirality : 0.043 0.810 2396 Planarity : 0.004 0.060 1855 Dihedral : 29.080 169.581 4056 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.47 % Allowed : 17.28 % Favored : 80.26 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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: 1.77 (0.25), residues: 1174 helix: 2.97 (0.22), residues: 530 sheet: 0.94 (0.34), residues: 236 loop : -1.22 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 126 TYR 0.010 0.001 TYR K 117 PHE 0.006 0.001 PHE A 169 TRP 0.007 0.001 TRP K 132 HIS 0.069 0.003 HIS L 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (14864) covalent geometry : angle 0.79051 / 0.47 (21099) SS BOND : bond 0.00806 / 0.41 ( 4) SS BOND : angle 4.71664 / 1.87 ( 8) hydrogen bonds : bond 0.04803 / 3.27 ( 661) hydrogen bonds : angle 3.27647 / 2.28 ( 1776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3780.43 seconds wall clock time: 65 minutes 23.43 seconds (3923.43 seconds total)