Starting phenix.real_space_refine on Thu Jul 31 20:21:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k78_22696/07_2025/7k78_22696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k78_22696/07_2025/7k78_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7k78_22696/07_2025/7k78_22696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k78_22696/07_2025/7k78_22696.map" model { file = "/net/cci-nas-00/data/ceres_data/7k78_22696/07_2025/7k78_22696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k78_22696/07_2025/7k78_22696.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.67, per 1000 atoms: 0.61 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: 3.48 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 6.04 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: 5.11 Time building geometry restraints manager: 4.21 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=" CA CYS K 181 " pdb=" CB CYS K 181 " ideal model delta sigma weight residual 1.527 1.553 -0.026 1.75e-02 3.27e+03 2.20e+00 bond pdb=" C3' DA J 225 " pdb=" O3' DA J 225 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CB ASN C 101 " pdb=" CG ASN C 101 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.81e+00 bond pdb=" CG LEU E 204 " pdb=" CD1 LEU E 204 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.61e+00 bond pdb=" C4' DA J 273 " pdb=" C3' DA J 273 " ideal model delta sigma weight residual 1.523 1.499 0.024 2.00e-02 2.50e+03 1.41e+00 ... (remaining 14859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 20157 1.56 - 3.12: 864 3.12 - 4.67: 63 4.67 - 6.23: 11 6.23 - 7.79: 4 Bond angle restraints: 21099 Sorted by residual: 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=" C TYR L 208 " pdb=" N ALA L 209 " pdb=" CA ALA L 209 " ideal model delta sigma weight residual 121.54 129.33 -7.79 1.91e+00 2.74e-01 1.66e+01 angle pdb=" C TYR K 208 " pdb=" N ALA K 209 " pdb=" CA ALA K 209 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" N LEU G 95 " pdb=" CA LEU G 95 " pdb=" C LEU G 95 " ideal model delta sigma weight residual 113.88 109.88 4.00 1.23e+00 6.61e-01 1.06e+01 angle pdb=" C ASN C 101 " pdb=" CA ASN C 101 " pdb=" CB ASN C 101 " ideal model delta sigma weight residual 111.73 116.67 -4.94 1.55e+00 4.16e-01 1.01e+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 - 0.033: 1619 0.033 - 0.065: 581 0.065 - 0.098: 123 0.098 - 0.131: 64 0.131 - 0.163: 9 Chirality restraints: 2396 Sorted by residual: chirality pdb=" CA ILE L 206 " pdb=" N ILE L 206 " pdb=" C ILE L 206 " pdb=" CB ILE L 206 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CB ILE K 206 " pdb=" CA ILE K 206 " pdb=" CG1 ILE K 206 " pdb=" CG2 ILE K 206 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CB THR K 50 " pdb=" CA THR K 50 " pdb=" OG1 THR K 50 " pdb=" CG2 THR K 50 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.21e-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: 0.760 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.550 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 0.044 14868 Z= 0.198 Angle : 0.698 7.791 21107 Z= 0.427 Chirality : 0.038 0.163 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.002 TRP K 132 HIS 0.006 0.001 HIS C 84 PHE 0.014 0.002 PHE A 169 TYR 0.022 0.002 TYR L 117 ARG 0.013 0.001 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.18738 ( 661) hydrogen bonds : angle 6.56541 ( 1776) SS BOND : bond 0.00466 ( 4) SS BOND : angle 4.42212 ( 8) covalent geometry : bond 0.00439 (14864) covalent geometry : angle 0.69259 (21099) *********************** 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 : 1.265 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: 0.3761 time to fit residues: 84.2125 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 : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN H 67 ASN K 170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.169479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116474 restraints weight = 15658.179| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.15 r_work: 0.2956 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1062 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= 0.193 Angle : 0.615 6.088 21107 Z= 0.361 Chirality : 0.037 0.154 2396 Planarity : 0.005 0.056 1855 Dihedral : 29.385 159.698 4056 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.79 % Allowed : 9.18 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1174 helix: 2.19 (0.23), residues: 528 sheet: 0.84 (0.33), residues: 236 loop : -1.55 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 132 HIS 0.004 0.001 HIS L 249 PHE 0.013 0.001 PHE A 169 TYR 0.014 0.002 TYR G 52 ARG 0.006 0.001 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.05706 ( 661) hydrogen bonds : angle 3.79432 ( 1776) SS BOND : bond 0.00286 ( 4) SS BOND : angle 2.05377 ( 8) covalent geometry : bond 0.00446 (14864) covalent geometry : angle 0.61357 (21099) *********************** 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 171 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: K 84 GLU cc_start: 0.8541 (tp30) cc_final: 0.8303 (mm-30) REVERT: K 160 ILE cc_start: 0.8726 (mt) cc_final: 0.8389 (mp) REVERT: K 219 ARG cc_start: 0.8257 (mtp180) cc_final: 0.7753 (mtm110) REVERT: K 251 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7518 (mp0) REVERT: L 65 GLN cc_start: 0.7899 (mp10) cc_final: 0.7306 (mp10) REVERT: L 68 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7905 (mm-30) outliers start: 8 outliers final: 4 residues processed: 165 average time/residue: 0.3485 time to fit residues: 77.1594 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 : 1.202 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN G 86 GLN H 67 ASN K 170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.172389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120288 restraints weight = 15739.587| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.16 r_work: 0.2985 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14868 Z= 0.151 Angle : 0.561 6.150 21107 Z= 0.331 Chirality : 0.035 0.146 2396 Planarity : 0.004 0.050 1855 Dihedral : 28.914 160.736 4056 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.28 % Allowed : 11.35 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1174 helix: 2.62 (0.22), residues: 529 sheet: 1.01 (0.34), residues: 236 loop : -1.40 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 132 HIS 0.003 0.001 HIS K 249 PHE 0.007 0.001 PHE B 101 TYR 0.009 0.001 TYR L 72 ARG 0.007 0.000 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 661) hydrogen bonds : angle 3.44893 ( 1776) SS BOND : bond 0.00165 ( 4) SS BOND : angle 1.10882 ( 8) covalent geometry : bond 0.00338 (14864) covalent geometry : angle 0.56106 (21099) *********************** 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 169 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.149 Fit side-chains REVERT: B 75 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8203 (mt-10) REVERT: D 75 GLU cc_start: 0.8343 (pp20) cc_final: 0.8031 (pt0) REVERT: K 84 GLU cc_start: 0.8553 (tp30) cc_final: 0.8333 (mm-30) REVERT: K 130 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7909 (p0) REVERT: K 160 ILE cc_start: 0.8691 (mt) cc_final: 0.8397 (mp) REVERT: K 214 ASP cc_start: 0.7624 (m-30) cc_final: 0.7316 (p0) REVERT: K 251 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7386 (mp0) REVERT: L 65 GLN cc_start: 0.7858 (mp10) cc_final: 0.7289 (mp10) REVERT: L 237 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7003 (mt-10) outliers start: 13 outliers final: 7 residues processed: 163 average time/residue: 0.3440 time to fit residues: 75.9159 Evaluate side-chains 157 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain C residue 64 ILE 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 33 LEU Chi-restraints excluded: chain L residue 170 HIS Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 89 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN G 86 GLN H 67 ASN K 61 GLN K 170 HIS L 170 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118361 restraints weight = 15965.050| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.31 r_work: 0.3022 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14868 Z= 0.161 Angle : 0.556 6.753 21107 Z= 0.328 Chirality : 0.035 0.145 2396 Planarity : 0.004 0.047 1855 Dihedral : 28.733 159.692 4056 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.37 % Allowed : 12.04 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1174 helix: 2.82 (0.22), residues: 530 sheet: 0.99 (0.34), residues: 236 loop : -1.32 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 132 HIS 0.004 0.001 HIS L 249 PHE 0.008 0.001 PHE A 169 TYR 0.009 0.001 TYR L 72 ARG 0.008 0.000 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 661) hydrogen bonds : angle 3.31460 ( 1776) SS BOND : bond 0.00223 ( 4) SS BOND : angle 1.31155 ( 8) covalent geometry : bond 0.00368 (14864) covalent geometry : angle 0.55522 (21099) *********************** 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 181 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: D 75 GLU cc_start: 0.8095 (pp20) cc_final: 0.7874 (pt0) REVERT: F 80 LYS cc_start: 0.8831 (mttm) cc_final: 0.8554 (mttt) REVERT: F 94 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8613 (mp10) REVERT: G 74 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8530 (t0) REVERT: K 164 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: L 65 GLN cc_start: 0.7972 (mp10) cc_final: 0.7459 (mp10) REVERT: L 111 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: L 237 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6946 (mt-10) outliers start: 24 outliers final: 18 residues processed: 171 average time/residue: 0.3289 time to fit residues: 76.3593 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 : 1.216 ------------------------------------------------------------------------------- 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 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 G residue 74 ASP 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 164 GLN Chi-restraints excluded: chain K residue 261 LYS Chi-restraints excluded: chain L residue 24 VAL 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 170 HIS Chi-restraints excluded: chain L residue 173 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 45 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 69 optimal weight: 0.0980 chunk 56 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN G 86 GLN H 67 ASN K 170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.166907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116509 restraints weight = 16020.868| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.36 r_work: 0.2987 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.004 0.041 14868 Z= 0.173 Angle : 0.558 5.891 21107 Z= 0.329 Chirality : 0.035 0.141 2396 Planarity : 0.004 0.046 1855 Dihedral : 28.681 160.516 4056 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.47 % Allowed : 12.64 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.25), residues: 1174 helix: 2.86 (0.22), residues: 530 sheet: 0.92 (0.34), residues: 236 loop : -1.27 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 132 HIS 0.006 0.001 HIS L 170 PHE 0.007 0.001 PHE A 158 TYR 0.010 0.001 TYR L 72 ARG 0.009 0.000 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 661) hydrogen bonds : angle 3.29362 ( 1776) SS BOND : bond 0.00197 ( 4) SS BOND : angle 1.48303 ( 8) covalent geometry : bond 0.00399 (14864) covalent geometry : angle 0.55725 (21099) *********************** 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 179 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.140 Fit side-chains REVERT: D 75 GLU cc_start: 0.8117 (pp20) cc_final: 0.7906 (pt0) REVERT: F 80 LYS cc_start: 0.8859 (mttm) cc_final: 0.8579 (mttt) REVERT: F 94 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8610 (mp10) REVERT: G 74 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8534 (t0) REVERT: K 251 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7265 (mp0) REVERT: L 65 GLN cc_start: 0.8001 (mp10) cc_final: 0.7432 (mp10) REVERT: L 111 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6782 (pp20) REVERT: L 237 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6936 (mt-10) outliers start: 25 outliers final: 20 residues processed: 168 average time/residue: 0.3266 time to fit residues: 74.6686 Evaluate side-chains 174 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 G residue 74 ASP 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 170 HIS Chi-restraints excluded: chain L residue 173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 125 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 71 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 18 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN G 86 GLN K 170 HIS L 170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.170812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121298 restraints weight = 16049.936| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.34 r_work: 0.2988 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14868 Z= 0.129 Angle : 0.526 5.947 21107 Z= 0.314 Chirality : 0.033 0.134 2396 Planarity : 0.004 0.039 1855 Dihedral : 28.503 162.052 4056 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.37 % Allowed : 13.43 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1174 helix: 3.09 (0.22), residues: 530 sheet: 1.02 (0.34), residues: 236 loop : -1.11 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 132 HIS 0.007 0.001 HIS L 170 PHE 0.005 0.001 PHE A 158 TYR 0.008 0.001 TYR G 59 ARG 0.006 0.000 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 661) hydrogen bonds : angle 3.18439 ( 1776) SS BOND : bond 0.00311 ( 4) SS BOND : angle 1.11789 ( 8) covalent geometry : bond 0.00275 (14864) covalent geometry : angle 0.52615 (21099) *********************** 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 176 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.277 Fit side-chains REVERT: D 72 ASP cc_start: 0.8755 (t0) cc_final: 0.8500 (t70) REVERT: D 75 GLU cc_start: 0.8061 (pp20) cc_final: 0.7785 (pt0) REVERT: F 80 LYS cc_start: 0.8826 (mttm) cc_final: 0.8541 (mttt) REVERT: F 94 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8639 (mp10) REVERT: G 74 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8508 (t0) REVERT: K 164 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: K 251 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7139 (mp0) REVERT: K 261 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7538 (tttp) REVERT: L 65 GLN cc_start: 0.7979 (mp10) cc_final: 0.7425 (mp10) REVERT: L 111 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: L 237 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6770 (mt-10) outliers start: 24 outliers final: 14 residues processed: 166 average time/residue: 0.3376 time to fit residues: 76.6366 Evaluate side-chains 164 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS 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 94 GLN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain K residue 25 GLN Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 164 GLN 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 170 HIS Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 223 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 108 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 116 optimal weight: 30.0000 chunk 91 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN G 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.163260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111350 restraints weight = 16050.147| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.52 r_work: 0.2937 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 14868 Z= 0.282 Angle : 0.635 6.929 21107 Z= 0.367 Chirality : 0.040 0.156 2396 Planarity : 0.005 0.049 1855 Dihedral : 28.885 158.922 4056 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.47 % Allowed : 14.81 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1174 helix: 2.60 (0.22), residues: 529 sheet: 0.85 (0.34), residues: 238 loop : -1.38 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 132 HIS 0.008 0.002 HIS L 170 PHE 0.010 0.002 PHE L 256 TYR 0.016 0.002 TYR D 125 ARG 0.007 0.001 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.05992 ( 661) hydrogen bonds : angle 3.46786 ( 1776) SS BOND : bond 0.00513 ( 4) SS BOND : angle 3.51267 ( 8) covalent geometry : bond 0.00672 (14864) covalent geometry : angle 0.63118 (21099) *********************** 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 173 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.460 Fit side-chains REVERT: D 75 GLU cc_start: 0.8157 (pp20) cc_final: 0.7923 (pt0) REVERT: F 94 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8512 (mp10) REVERT: K 251 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7447 (mp0) REVERT: K 261 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7562 (tttp) REVERT: L 65 GLN cc_start: 0.8055 (mp10) cc_final: 0.7480 (mp10) REVERT: L 237 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7075 (mt-10) outliers start: 25 outliers final: 18 residues processed: 163 average time/residue: 0.3520 time to fit residues: 78.3059 Evaluate side-chains 167 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 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 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 33 LEU Chi-restraints excluded: chain L residue 92 LEU 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 Chi-restraints excluded: chain L residue 223 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 96 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN 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 = 0.171346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121712 restraints weight = 16124.494| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.27 r_work: 0.2919 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14868 Z= 0.136 Angle : 0.558 9.307 21107 Z= 0.329 Chirality : 0.035 0.165 2396 Planarity : 0.004 0.049 1855 Dihedral : 28.715 163.446 4056 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.88 % Allowed : 16.09 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.25), residues: 1174 helix: 3.04 (0.22), residues: 529 sheet: 1.00 (0.34), residues: 236 loop : -1.18 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 132 HIS 0.003 0.001 HIS C 84 PHE 0.006 0.001 PHE A 169 TYR 0.019 0.001 TYR A 145 ARG 0.008 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 661) hydrogen bonds : angle 3.26518 ( 1776) SS BOND : bond 0.00335 ( 4) SS BOND : angle 1.55372 ( 8) covalent geometry : bond 0.00292 (14864) covalent geometry : angle 0.55763 (21099) *********************** 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 164 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.372 Fit side-chains REVERT: D 75 GLU cc_start: 0.8309 (pp20) cc_final: 0.7946 (pt0) REVERT: F 80 LYS cc_start: 0.8725 (mttm) cc_final: 0.8387 (mttt) REVERT: F 94 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8593 (mp10) REVERT: K 251 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7478 (mp0) REVERT: K 261 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7321 (tttt) REVERT: L 65 GLN cc_start: 0.7822 (mp10) cc_final: 0.7197 (mp10) REVERT: L 237 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6818 (mt-10) outliers start: 19 outliers final: 15 residues processed: 157 average time/residue: 0.5395 time to fit residues: 114.8746 Evaluate side-chains 161 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS 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 F residue 94 GLN 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 33 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 92 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 132 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN G 86 GLN K 170 HIS L 170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.165272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.114089 restraints weight = 15887.092| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.29 r_work: 0.2973 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14868 Z= 0.217 Angle : 0.590 8.640 21107 Z= 0.343 Chirality : 0.037 0.149 2396 Planarity : 0.004 0.045 1855 Dihedral : 28.728 160.712 4056 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.97 % Allowed : 16.09 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1174 helix: 2.82 (0.22), residues: 529 sheet: 0.95 (0.34), residues: 236 loop : -1.33 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 132 HIS 0.005 0.001 HIS L 249 PHE 0.009 0.002 PHE L 229 TYR 0.019 0.002 TYR H 46 ARG 0.008 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.05222 ( 661) hydrogen bonds : angle 3.34591 ( 1776) SS BOND : bond 0.00357 ( 4) SS BOND : angle 2.65682 ( 8) covalent geometry : bond 0.00514 (14864) covalent geometry : angle 0.58752 (21099) *********************** 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 165 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.214 Fit side-chains REVERT: D 75 GLU cc_start: 0.8098 (pp20) cc_final: 0.7840 (pt0) REVERT: F 80 LYS cc_start: 0.8842 (mttm) cc_final: 0.8542 (mttt) REVERT: F 94 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8614 (mp10) REVERT: K 251 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7493 (mp0) REVERT: K 261 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7563 (tttp) REVERT: L 65 GLN cc_start: 0.8052 (mp10) cc_final: 0.7480 (mp10) REVERT: L 237 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6979 (mt-10) outliers start: 20 outliers final: 16 residues processed: 158 average time/residue: 0.3366 time to fit residues: 72.0709 Evaluate side-chains 161 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS 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 F residue 94 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 33 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 92 LEU 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 Chi-restraints excluded: chain L residue 223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN K 25 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 = 0.3858 r_free = 0.3858 target = 0.166438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116004 restraints weight = 15903.641| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.37 r_work: 0.2970 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14868 Z= 0.176 Angle : 0.573 12.846 21107 Z= 0.334 Chirality : 0.035 0.151 2396 Planarity : 0.004 0.041 1855 Dihedral : 28.648 162.688 4056 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.88 % Allowed : 16.09 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.25), residues: 1174 helix: 2.88 (0.22), residues: 529 sheet: 0.99 (0.34), residues: 236 loop : -1.27 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 132 HIS 0.004 0.001 HIS L 249 PHE 0.007 0.001 PHE A 158 TYR 0.012 0.001 TYR A 145 ARG 0.008 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 661) hydrogen bonds : angle 3.31446 ( 1776) SS BOND : bond 0.00352 ( 4) SS BOND : angle 3.57287 ( 8) covalent geometry : bond 0.00408 (14864) covalent geometry : angle 0.56910 (21099) ********************** 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 162 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.397 Fit side-chains REVERT: D 75 GLU cc_start: 0.8145 (pp20) cc_final: 0.7874 (pt0) REVERT: F 80 LYS cc_start: 0.8855 (mttm) cc_final: 0.8559 (mttt) REVERT: F 94 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8632 (mp10) REVERT: K 251 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7440 (mp0) REVERT: K 261 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7499 (tttp) REVERT: L 237 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6984 (mt-10) outliers start: 19 outliers final: 16 residues processed: 157 average time/residue: 0.4018 time to fit residues: 87.2508 Evaluate side-chains 160 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain B residue 51 ILE 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 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 33 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 82 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 chunk 60 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 170 HIS ** L 170 HIS ** 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 = 0.3859 r_free = 0.3859 target = 0.166538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.115567 restraints weight = 16026.576| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.40 r_work: 0.2987 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.226 14868 Z= 0.245 Angle : 0.868 59.199 21107 Z= 0.532 Chirality : 0.038 0.645 2396 Planarity : 0.007 0.200 1855 Dihedral : 28.653 162.679 4056 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.68 % Allowed : 16.39 % Favored : 81.93 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1174 helix: 2.90 (0.22), residues: 529 sheet: 0.99 (0.34), residues: 236 loop : -1.26 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 132 HIS 0.022 0.002 HIS L 170 PHE 0.007 0.001 PHE A 158 TYR 0.011 0.001 TYR K 117 ARG 0.007 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 661) hydrogen bonds : angle 3.31344 ( 1776) SS BOND : bond 0.01368 ( 4) SS BOND : angle 3.22066 ( 8) covalent geometry : bond 0.00545 (14864) covalent geometry : angle 0.86564 (21099) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7815.51 seconds wall clock time: 140 minutes 25.43 seconds (8425.43 seconds total)