Starting phenix.real_space_refine on Sat Feb 7 19:59:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d4u_46570/02_2026/9d4u_46570.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d4u_46570/02_2026/9d4u_46570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d4u_46570/02_2026/9d4u_46570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d4u_46570/02_2026/9d4u_46570.map" model { file = "/net/cci-nas-00/data/ceres_data/9d4u_46570/02_2026/9d4u_46570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d4u_46570/02_2026/9d4u_46570.cif" } resolution = 3.55 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= 0.009 sd= 0.349 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 S 55 5.16 5 C 11156 2.51 5 N 2972 2.21 5 O 3437 1.98 5 H 17597 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35217 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3791 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 231} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3723 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain: "C" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3580 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 4, 'TRANS': 225} Chain: "D" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3550 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 9, 'TRANS': 217} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3486 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 4, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3464 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3762 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 9, 'TRANS': 235} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3008 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 4 Chain: "J" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2771 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 2848 Classifications: {'peptide': 176} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 1 Chain: "P" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1234 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} 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 Time building chain proxies: 6.08, per 1000 atoms: 0.17 Number of scatterers: 35217 At special positions: 0 Unit cell: (137.772, 140.976, 124.956, 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 55 16.00 O 3437 8.00 N 2972 7.00 C 11156 6.00 H 17597 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 961.8 milliseconds 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4204 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 40.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 removed outlier: 4.424A pdb=" N HIS A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 15' Processing helix chain 'A' and resid 25 through 34 removed outlier: 3.732A pdb=" N ALA A 31 " --> pdb=" O GLN A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.795A pdb=" N VAL A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 86 through 109 removed outlier: 3.727A pdb=" N TYR A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 129 removed outlier: 3.557A pdb=" N ILE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 removed outlier: 4.447A pdb=" N LYS A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 Processing helix chain 'A' and resid 237 through 252 removed outlier: 3.967A pdb=" N GLU A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.806A pdb=" N TYR B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 removed outlier: 8.165A pdb=" N LEU B 61 " --> pdb=" O MET B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 57 through 61' Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.532A pdb=" N LYS B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.695A pdb=" N GLN B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 199 removed outlier: 3.565A pdb=" N GLU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 222 No H-bonds generated for 'chain 'B' and resid 219 through 222' Processing helix chain 'B' and resid 239 through 249 removed outlier: 3.794A pdb=" N ARG B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 30 Processing helix chain 'C' and resid 80 through 103 removed outlier: 3.986A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 125 removed outlier: 3.705A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N HIS C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 4.456A pdb=" N MET C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 200 removed outlier: 3.927A pdb=" N GLU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 78 through 100 Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.914A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.838A pdb=" N THR D 195 " --> pdb=" O CYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 210 removed outlier: 5.191A pdb=" N ILE D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 206 through 210' Processing helix chain 'D' and resid 225 through 246 removed outlier: 3.837A pdb=" N ASN D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN D 235 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLN D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 29 removed outlier: 4.027A pdb=" N SER E 27 " --> pdb=" O GLN E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 84 through 104 removed outlier: 3.558A pdb=" N MET E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 187 removed outlier: 4.147A pdb=" N GLU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TRP E 187 " --> pdb=" O LEU E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 207 removed outlier: 3.553A pdb=" N ALA E 196 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN E 206 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL E 207 " --> pdb=" O ILE E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 249 removed outlier: 4.813A pdb=" N ALA E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA E 249 " --> pdb=" O GLU E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 28 Processing helix chain 'F' and resid 77 through 99 removed outlier: 3.664A pdb=" N SER F 95 " --> pdb=" O GLN F 91 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 122 removed outlier: 3.595A pdb=" N GLN F 117 " --> pdb=" O CYS F 113 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 175 removed outlier: 3.503A pdb=" N LYS F 169 " --> pdb=" O SER F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 201 removed outlier: 3.846A pdb=" N LEU F 201 " --> pdb=" O ILE F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 231 No H-bonds generated for 'chain 'F' and resid 228 through 231' Processing helix chain 'G' and resid 21 through 33 removed outlier: 3.593A pdb=" N GLU G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA G 27 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 removed outlier: 4.225A pdb=" N GLY G 85 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS G 87 " --> pdb=" O PRO G 83 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 122 removed outlier: 3.775A pdb=" N ARG G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.770A pdb=" N ALA G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS G 182 " --> pdb=" O LYS G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 204 removed outlier: 3.520A pdb=" N LYS G 198 " --> pdb=" O LYS G 194 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS G 204 " --> pdb=" O ILE G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 248 removed outlier: 4.279A pdb=" N LYS G 245 " --> pdb=" O ASP G 241 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE G 247 " --> pdb=" O ALA G 243 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN G 248 " --> pdb=" O GLN G 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 100 Processing helix chain 'I' and resid 104 through 119 Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.979A pdb=" N ALA I 163 " --> pdb=" O GLY I 159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 79 removed outlier: 3.765A pdb=" N GLU J 79 " --> pdb=" O LYS J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 154 removed outlier: 6.405A pdb=" N LEU J 146 " --> pdb=" O ALA J 142 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 175 Processing helix chain 'K' and resid 51 through 72 removed outlier: 4.415A pdb=" N ALA K 57 " --> pdb=" O THR K 53 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU K 58 " --> pdb=" O VAL K 54 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP K 72 " --> pdb=" O SER K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 90 removed outlier: 3.553A pdb=" N VAL K 80 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG K 85 " --> pdb=" O SER K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 148 removed outlier: 3.825A pdb=" N THR K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 172 removed outlier: 3.773A pdb=" N GLU K 169 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS K 170 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 58 removed outlier: 5.779A pdb=" N SER P 55 " --> pdb=" O HIS P 51 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N THR P 56 " --> pdb=" O PRO P 52 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS P 58 " --> pdb=" O GLU P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 76 removed outlier: 3.607A pdb=" N ARG P 65 " --> pdb=" O GLU P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 95 removed outlier: 4.725A pdb=" N THR P 94 " --> pdb=" O ILE P 90 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP P 95 " --> pdb=" O VAL P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 112 removed outlier: 3.902A pdb=" N ILE P 109 " --> pdb=" O ILE P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 123 569 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.30 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 5187 1.04 - 1.23: 14428 1.23 - 1.43: 5499 1.43 - 1.63: 10316 1.63 - 1.82: 87 Bond restraints: 35517 Sorted by residual: bond pdb=" N ASN I 12 " pdb=" H ASN I 12 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" N MET A 121 " pdb=" H MET A 121 " ideal model delta sigma weight residual 0.860 1.014 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" N ALA D 223 " pdb=" H ALA D 223 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CZ3 TRP E 187 " pdb=" HZ3 TRP E 187 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CD2 TYR K 121 " pdb=" HD2 TYR K 121 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.75e+01 ... (remaining 35512 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 62288 5.41 - 10.83: 1920 10.83 - 16.24: 20 16.24 - 21.66: 0 21.66 - 27.07: 1 Bond angle restraints: 64229 Sorted by residual: angle pdb=" CA ARG E 132 " pdb=" N ARG E 132 " pdb=" H ARG E 132 " ideal model delta sigma weight residual 114.00 141.07 -27.07 3.00e+00 1.11e-01 8.14e+01 angle pdb=" CB HIS D 96 " pdb=" CG HIS D 96 " pdb=" CD2 HIS D 96 " ideal model delta sigma weight residual 131.20 124.71 6.49 1.30e+00 5.92e-01 2.49e+01 angle pdb=" N GLN I 120 " pdb=" CA GLN I 120 " pdb=" C GLN I 120 " ideal model delta sigma weight residual 111.90 118.48 -6.58 1.32e+00 5.74e-01 2.48e+01 angle pdb=" CB HIS K 146 " pdb=" CG HIS K 146 " pdb=" CD2 HIS K 146 " ideal model delta sigma weight residual 131.20 124.81 6.39 1.30e+00 5.92e-01 2.41e+01 angle pdb=" N PHE I 6 " pdb=" CA PHE I 6 " pdb=" C PHE I 6 " ideal model delta sigma weight residual 113.20 119.09 -5.89 1.21e+00 6.83e-01 2.37e+01 ... (remaining 64224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 15059 17.78 - 35.55: 1086 35.55 - 53.33: 338 53.33 - 71.11: 119 71.11 - 88.89: 27 Dihedral angle restraints: 16629 sinusoidal: 9095 harmonic: 7534 Sorted by residual: dihedral pdb=" CA LYS K 113 " pdb=" C LYS K 113 " pdb=" N PRO K 114 " pdb=" CA PRO K 114 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASN E 108 " pdb=" C ASN E 108 " pdb=" N VAL E 109 " pdb=" CA VAL E 109 " ideal model delta harmonic sigma weight residual 180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ILE K 183 " pdb=" C ILE K 183 " pdb=" N VAL K 184 " pdb=" CA VAL K 184 " ideal model delta harmonic sigma weight residual 180.00 150.89 29.11 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 16626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1865 0.099 - 0.197: 766 0.197 - 0.296: 127 0.296 - 0.394: 11 0.394 - 0.493: 3 Chirality restraints: 2772 Sorted by residual: chirality pdb=" CA GLU G 209 " pdb=" N GLU G 209 " pdb=" C GLU G 209 " pdb=" CB GLU G 209 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CA TYR D 156 " pdb=" N TYR D 156 " pdb=" C TYR D 156 " pdb=" CB TYR D 156 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CA TYR F 225 " pdb=" N TYR F 225 " pdb=" C TYR F 225 " pdb=" CB TYR F 225 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 2769 not shown) Planarity restraints: 5297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN I 189 " -0.192 2.00e-02 2.50e+03 2.17e-01 7.05e+02 pdb=" CD GLN I 189 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN I 189 " 0.187 2.00e-02 2.50e+03 pdb=" NE2 GLN I 189 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN I 189 " 0.324 2.00e-02 2.50e+03 pdb="HE22 GLN I 189 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 119 " 0.136 2.00e-02 2.50e+03 8.02e-02 2.57e+02 pdb=" CG TRP P 119 " 0.110 2.00e-02 2.50e+03 pdb=" CD1 TRP P 119 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP P 119 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP P 119 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP P 119 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP P 119 " -0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 119 " 0.044 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 119 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP P 119 " 0.050 2.00e-02 2.50e+03 pdb=" HD1 TRP P 119 " -0.033 2.00e-02 2.50e+03 pdb=" HE1 TRP P 119 " -0.163 2.00e-02 2.50e+03 pdb=" HE3 TRP P 119 " -0.140 2.00e-02 2.50e+03 pdb=" HZ2 TRP P 119 " 0.062 2.00e-02 2.50e+03 pdb=" HZ3 TRP P 119 " -0.063 2.00e-02 2.50e+03 pdb=" HH2 TRP P 119 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 234 " 0.254 9.50e-02 1.11e+02 1.29e-01 2.18e+02 pdb=" NE ARG B 234 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 234 " -0.086 2.00e-02 2.50e+03 pdb=" NH1 ARG B 234 " -0.109 2.00e-02 2.50e+03 pdb=" NH2 ARG B 234 " -0.090 2.00e-02 2.50e+03 pdb="HH11 ARG B 234 " 0.046 2.00e-02 2.50e+03 pdb="HH12 ARG B 234 " 0.145 2.00e-02 2.50e+03 pdb="HH21 ARG B 234 " 0.167 2.00e-02 2.50e+03 pdb="HH22 ARG B 234 " -0.077 2.00e-02 2.50e+03 ... (remaining 5294 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 2205 2.17 - 2.78: 63279 2.78 - 3.38: 101104 3.38 - 3.99: 132332 3.99 - 4.60: 196058 Nonbonded interactions: 494978 Sorted by model distance: nonbonded pdb=" HG CYS F 113 " pdb="HG12 VAL F 153 " model vdw 1.561 2.440 nonbonded pdb="HH22 ARG A 131 " pdb=" HG SER P 104 " model vdw 1.583 2.100 nonbonded pdb=" OD2 ASP K 11 " pdb=" HG1 THR K 154 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP G 44 " pdb=" HG SER G 220 " model vdw 1.603 2.450 nonbonded pdb=" HG1 THR B 68 " pdb=" OD1 ASP B 70 " model vdw 1.612 2.450 ... (remaining 494973 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 2.470 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: 0.230 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.650 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 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 : 0.012 0.046 17920 Z= 0.756 Angle : 1.927 8.108 24238 Z= 1.280 Chirality : 0.101 0.493 2772 Planarity : 0.013 0.123 3118 Dihedral : 14.546 87.510 6611 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.90 % Allowed : 7.00 % Favored : 91.10 % Cbeta Deviations : 0.29 % 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: -2.54 (0.15), residues: 2235 helix: -1.93 (0.14), residues: 874 sheet: -0.29 (0.24), residues: 383 loop : -1.91 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 234 TYR 0.108 0.018 TYR P 123 PHE 0.093 0.014 PHE J 87 TRP 0.119 0.025 TRP J 183 HIS 0.019 0.003 HIS K 146 Details of bonding type rmsd covalent geometry : bond 0.01210 (17920) covalent geometry : angle 1.92750 (24238) hydrogen bonds : bond 0.20591 ( 569) hydrogen bonds : angle 8.21307 ( 1707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 62 is missing expected H atoms. Skipping. Evaluate side-chains 551 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 515 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 SER cc_start: 0.8977 (m) cc_final: 0.7678 (p) REVERT: A 147 ASP cc_start: 0.7506 (t0) cc_final: 0.6869 (t70) REVERT: A 251 GLN cc_start: 0.8781 (tt0) cc_final: 0.8452 (tm-30) REVERT: B 13 SER cc_start: 0.9183 (m) cc_final: 0.8765 (p) REVERT: B 96 SER cc_start: 0.8987 (m) cc_final: 0.8738 (p) REVERT: B 108 LYS cc_start: 0.8352 (tptm) cc_final: 0.7968 (tttt) REVERT: B 113 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8461 (mm-30) REVERT: B 231 LYS cc_start: 0.8626 (mttt) cc_final: 0.8235 (mtmt) REVERT: B 241 GLN cc_start: 0.8816 (tp40) cc_final: 0.8389 (tp-100) REVERT: C 120 GLN cc_start: 0.7812 (tm-30) cc_final: 0.7608 (tp-100) REVERT: C 122 TYR cc_start: 0.8087 (m-80) cc_final: 0.7877 (m-10) REVERT: C 244 ILE cc_start: 0.1450 (OUTLIER) cc_final: 0.1119 (mp) REVERT: D 149 GLN cc_start: 0.6085 (OUTLIER) cc_final: 0.5828 (tm-30) REVERT: D 239 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8200 (mt-10) REVERT: E 76 CYS cc_start: 0.7885 (m) cc_final: 0.7651 (m) REVERT: F 39 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.5714 (ptm-80) REVERT: F 178 THR cc_start: 0.7366 (p) cc_final: 0.6662 (p) REVERT: I 82 GLU cc_start: 0.8914 (tp30) cc_final: 0.8685 (tp30) REVERT: I 246 ILE cc_start: 0.9016 (mt) cc_final: 0.8781 (tp) REVERT: J 75 LYS cc_start: 0.8658 (tttm) cc_final: 0.8243 (tppt) REVERT: J 149 MET cc_start: 0.8692 (mmm) cc_final: 0.8485 (tpp) REVERT: J 173 ASN cc_start: 0.7700 (m-40) cc_final: 0.6578 (m110) REVERT: K 3 ILE cc_start: 0.7399 (pt) cc_final: 0.7006 (pt) REVERT: K 111 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8672 (mmmm) REVERT: K 127 GLU cc_start: 0.8127 (mp0) cc_final: 0.7755 (tm-30) REVERT: P 65 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5005 (tmm-80) REVERT: P 112 ASN cc_start: 0.7340 (m110) cc_final: 0.6600 (m110) outliers start: 36 outliers final: 15 residues processed: 544 average time/residue: 0.4581 time to fit residues: 336.5979 Evaluate side-chains 406 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 387 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain P residue 65 ARG Chi-restraints excluded: chain P residue 91 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 240 ASN B 218 ASN C 124 GLN D 94 GLN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN E 73 HIS F 41 ASN ** I 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 ASN K 146 HIS K 147 HIS P 51 HIS ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.082166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.073943 restraints weight = 222534.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.076704 restraints weight = 90153.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.078353 restraints weight = 45388.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.079330 restraints weight = 26153.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.079969 restraints weight = 16675.434| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17920 Z= 0.163 Angle : 0.694 7.536 24238 Z= 0.384 Chirality : 0.045 0.178 2772 Planarity : 0.005 0.043 3118 Dihedral : 8.225 87.084 2496 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.47 % Allowed : 13.01 % Favored : 84.52 % 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: -1.75 (0.16), residues: 2235 helix: -0.82 (0.16), residues: 866 sheet: -0.90 (0.22), residues: 475 loop : -1.48 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 93 TYR 0.018 0.002 TYR F 87 PHE 0.015 0.002 PHE I 37 TRP 0.011 0.001 TRP D 159 HIS 0.013 0.002 HIS I 170 Details of bonding type rmsd covalent geometry : bond 0.00347 (17920) covalent geometry : angle 0.69384 (24238) hydrogen bonds : bond 0.06103 ( 569) hydrogen bonds : angle 5.50229 ( 1707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 62 is missing expected H atoms. Skipping. Evaluate side-chains 461 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 414 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8873 (mmm) cc_final: 0.8509 (mmm) REVERT: B 13 SER cc_start: 0.9121 (m) cc_final: 0.8908 (p) REVERT: B 108 LYS cc_start: 0.8065 (tptm) cc_final: 0.7766 (tttt) REVERT: B 174 PHE cc_start: 0.7221 (t80) cc_final: 0.6901 (t80) REVERT: B 181 ASP cc_start: 0.8114 (t0) cc_final: 0.7888 (t0) REVERT: D 149 GLN cc_start: 0.5824 (OUTLIER) cc_final: 0.5511 (tm-30) REVERT: E 239 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8740 (mm) REVERT: F 178 THR cc_start: 0.7138 (p) cc_final: 0.6822 (p) REVERT: F 188 GLU cc_start: 0.7666 (tt0) cc_final: 0.7403 (tt0) REVERT: G 78 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.8332 (p90) REVERT: I 86 GLN cc_start: 0.8138 (mm110) cc_final: 0.7920 (mm110) REVERT: I 174 ASP cc_start: 0.8427 (m-30) cc_final: 0.8057 (m-30) REVERT: J 75 LYS cc_start: 0.8450 (tttm) cc_final: 0.8145 (tppt) REVERT: J 135 ASP cc_start: 0.5976 (t0) cc_final: 0.5450 (t0) REVERT: J 173 ASN cc_start: 0.8186 (m110) cc_final: 0.7604 (m110) REVERT: K 85 ARG cc_start: 0.7754 (ptm-80) cc_final: 0.7459 (tmt-80) REVERT: K 107 TYR cc_start: 0.8381 (t80) cc_final: 0.7559 (t80) REVERT: P 65 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8138 (tmm-80) outliers start: 47 outliers final: 25 residues processed: 442 average time/residue: 0.4435 time to fit residues: 266.8242 Evaluate side-chains 372 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 343 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain P residue 65 ARG Chi-restraints excluded: chain P residue 119 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 16 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 144 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 69 optimal weight: 0.0060 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS D 178 ASN G 23 GLN G 68 GLN I 10 GLN I 114 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.081140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.072918 restraints weight = 221764.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.075667 restraints weight = 89359.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.077316 restraints weight = 44736.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.078294 restraints weight = 25581.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.078922 restraints weight = 16212.806| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17920 Z= 0.138 Angle : 0.624 6.735 24238 Z= 0.340 Chirality : 0.043 0.157 2772 Planarity : 0.004 0.046 3118 Dihedral : 7.104 89.781 2477 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.26 % Allowed : 15.27 % Favored : 82.46 % 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: -1.28 (0.17), residues: 2235 helix: -0.18 (0.17), residues: 873 sheet: -1.01 (0.22), residues: 475 loop : -1.28 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 93 TYR 0.024 0.001 TYR A 155 PHE 0.017 0.001 PHE G 242 TRP 0.010 0.001 TRP D 159 HIS 0.008 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00298 (17920) covalent geometry : angle 0.62444 (24238) hydrogen bonds : bond 0.04958 ( 569) hydrogen bonds : angle 5.01751 ( 1707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 62 is missing expected H atoms. Skipping. Evaluate side-chains 419 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 376 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8263 (tm-30) cc_final: 0.8051 (tm-30) REVERT: A 175 GLN cc_start: 0.6995 (pm20) cc_final: 0.6751 (pm20) REVERT: B 13 SER cc_start: 0.9111 (m) cc_final: 0.8784 (p) REVERT: B 108 LYS cc_start: 0.8043 (tptm) cc_final: 0.7767 (tttt) REVERT: B 123 GLN cc_start: 0.8177 (mt0) cc_final: 0.7923 (tt0) REVERT: B 181 ASP cc_start: 0.8305 (t0) cc_final: 0.8102 (t0) REVERT: D 149 GLN cc_start: 0.5826 (OUTLIER) cc_final: 0.5375 (tm-30) REVERT: F 178 THR cc_start: 0.7303 (p) cc_final: 0.6914 (p) REVERT: F 188 GLU cc_start: 0.7740 (tt0) cc_final: 0.7451 (tt0) REVERT: G 78 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8411 (p90) REVERT: I 86 GLN cc_start: 0.8180 (mm110) cc_final: 0.7915 (mm110) REVERT: I 174 ASP cc_start: 0.8275 (m-30) cc_final: 0.7994 (m-30) REVERT: J 75 LYS cc_start: 0.8386 (tttm) cc_final: 0.8075 (tppt) REVERT: J 153 LEU cc_start: 0.8432 (tp) cc_final: 0.8171 (tp) REVERT: J 173 ASN cc_start: 0.7929 (m110) cc_final: 0.7673 (m110) REVERT: P 65 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8343 (tmm-80) outliers start: 43 outliers final: 26 residues processed: 400 average time/residue: 0.4405 time to fit residues: 239.2581 Evaluate side-chains 375 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 346 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 78 TYR Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 10 GLN Chi-restraints excluded: chain I residue 219 TYR Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain P residue 65 ARG Chi-restraints excluded: chain P residue 119 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 30 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN E 154 GLN ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 248 ASN I 10 GLN I 114 GLN P 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.077807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.069736 restraints weight = 224373.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.072394 restraints weight = 90841.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.073986 restraints weight = 45656.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.074949 restraints weight = 26314.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.075559 restraints weight = 16810.879| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17920 Z= 0.208 Angle : 0.651 8.316 24238 Z= 0.356 Chirality : 0.043 0.152 2772 Planarity : 0.005 0.051 3118 Dihedral : 6.817 80.981 2473 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.53 % Allowed : 15.85 % Favored : 81.62 % 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: -1.35 (0.17), residues: 2235 helix: -0.06 (0.17), residues: 877 sheet: -1.17 (0.22), residues: 478 loop : -1.46 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 93 TYR 0.029 0.002 TYR D 156 PHE 0.018 0.002 PHE G 242 TRP 0.013 0.002 TRP D 159 HIS 0.010 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00454 (17920) covalent geometry : angle 0.65062 (24238) hydrogen bonds : bond 0.04882 ( 569) hydrogen bonds : angle 5.00138 ( 1707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 62 is missing expected H atoms. Skipping. Evaluate side-chains 392 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 344 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.7365 (pm20) cc_final: 0.7056 (pm20) REVERT: B 108 LYS cc_start: 0.8154 (tptm) cc_final: 0.7875 (tttt) REVERT: B 181 ASP cc_start: 0.8401 (t0) cc_final: 0.8071 (t0) REVERT: I 86 GLN cc_start: 0.8157 (mm110) cc_final: 0.7905 (mm110) REVERT: I 174 ASP cc_start: 0.8483 (m-30) cc_final: 0.8118 (m-30) REVERT: I 207 MET cc_start: 0.8138 (mpp) cc_final: 0.7893 (mpp) REVERT: J 75 LYS cc_start: 0.8437 (tttm) cc_final: 0.8174 (tppt) REVERT: P 65 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8442 (tmm-80) outliers start: 48 outliers final: 37 residues processed: 372 average time/residue: 0.4674 time to fit residues: 234.8873 Evaluate side-chains 368 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 330 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 219 TYR Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain P residue 65 ARG Chi-restraints excluded: chain P residue 119 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 151 optimal weight: 0.0570 chunk 99 optimal weight: 0.7980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN G 68 GLN ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.079733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.071558 restraints weight = 222896.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.074292 restraints weight = 89955.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.075902 restraints weight = 45028.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.076871 restraints weight = 25892.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.077489 restraints weight = 16491.865| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17920 Z= 0.121 Angle : 0.582 7.265 24238 Z= 0.311 Chirality : 0.042 0.150 2772 Planarity : 0.004 0.052 3118 Dihedral : 6.036 74.606 2462 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.16 % Allowed : 17.06 % Favored : 80.78 % 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: -1.03 (0.17), residues: 2235 helix: 0.37 (0.17), residues: 870 sheet: -1.15 (0.23), residues: 471 loop : -1.36 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 126 TYR 0.019 0.001 TYR E 102 PHE 0.018 0.001 PHE D 75 TRP 0.011 0.001 TRP D 159 HIS 0.006 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00271 (17920) covalent geometry : angle 0.58169 (24238) hydrogen bonds : bond 0.04233 ( 569) hydrogen bonds : angle 4.65430 ( 1707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 62 is missing expected H atoms. Skipping. Evaluate side-chains 383 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 342 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.7350 (pm20) cc_final: 0.6994 (pm20) REVERT: B 108 LYS cc_start: 0.7950 (tptm) cc_final: 0.7690 (tttt) REVERT: F 188 GLU cc_start: 0.7641 (tt0) cc_final: 0.7405 (tt0) REVERT: I 86 GLN cc_start: 0.8160 (mm110) cc_final: 0.7816 (mm110) REVERT: I 174 ASP cc_start: 0.8374 (m-30) cc_final: 0.8016 (m-30) REVERT: J 75 LYS cc_start: 0.8375 (tttm) cc_final: 0.8109 (tppt) REVERT: K 187 ASP cc_start: 0.8007 (p0) cc_final: 0.7375 (p0) outliers start: 41 outliers final: 31 residues processed: 368 average time/residue: 0.4310 time to fit residues: 215.5642 Evaluate side-chains 355 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 324 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain P residue 88 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 26 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.072636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.064823 restraints weight = 229018.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.067374 restraints weight = 92379.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.068911 restraints weight = 46349.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.069842 restraints weight = 26718.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.070432 restraints weight = 17145.224| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17920 Z= 0.226 Angle : 0.657 6.990 24238 Z= 0.359 Chirality : 0.043 0.154 2772 Planarity : 0.005 0.070 3118 Dihedral : 6.165 64.655 2458 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.21 % Allowed : 17.59 % Favored : 79.20 % 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: -1.38 (0.17), residues: 2235 helix: 0.09 (0.17), residues: 884 sheet: -1.32 (0.22), residues: 476 loop : -1.61 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 126 TYR 0.030 0.002 TYR D 156 PHE 0.017 0.002 PHE D 75 TRP 0.014 0.002 TRP D 159 HIS 0.011 0.002 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00496 (17920) covalent geometry : angle 0.65687 (24238) hydrogen bonds : bond 0.04729 ( 569) hydrogen bonds : angle 4.91954 ( 1707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 62 is missing expected H atoms. Skipping. Evaluate side-chains 385 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 324 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.7576 (pm20) cc_final: 0.7198 (pm20) REVERT: B 108 LYS cc_start: 0.8194 (tptm) cc_final: 0.7892 (tttt) REVERT: C 244 ILE cc_start: 0.1448 (OUTLIER) cc_final: 0.1245 (mp) REVERT: I 86 GLN cc_start: 0.8137 (mm110) cc_final: 0.7869 (mm110) REVERT: I 174 ASP cc_start: 0.8511 (m-30) cc_final: 0.8173 (m-30) REVERT: I 207 MET cc_start: 0.7906 (mpp) cc_final: 0.7631 (mpp) REVERT: I 244 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7680 (tm-30) REVERT: J 75 LYS cc_start: 0.8497 (tttm) cc_final: 0.8204 (tppt) REVERT: P 65 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8593 (tmm-80) REVERT: P 119 TRP cc_start: 0.8126 (OUTLIER) cc_final: 0.7925 (m100) outliers start: 61 outliers final: 51 residues processed: 361 average time/residue: 0.4545 time to fit residues: 223.4085 Evaluate side-chains 366 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 312 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 219 TYR Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain P residue 65 ARG Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain P residue 119 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 chunk 219 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.073980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.066120 restraints weight = 227598.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.068722 restraints weight = 90952.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.070286 restraints weight = 45204.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.071226 restraints weight = 25795.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.071815 restraints weight = 16418.318| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17920 Z= 0.132 Angle : 0.591 6.714 24238 Z= 0.316 Chirality : 0.042 0.148 2772 Planarity : 0.004 0.053 3118 Dihedral : 5.802 58.238 2458 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.37 % Allowed : 19.06 % Favored : 78.57 % 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: -1.13 (0.17), residues: 2235 helix: 0.40 (0.17), residues: 874 sheet: -1.26 (0.22), residues: 475 loop : -1.54 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 93 TYR 0.021 0.001 TYR A 155 PHE 0.021 0.001 PHE D 75 TRP 0.013 0.001 TRP D 159 HIS 0.008 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00296 (17920) covalent geometry : angle 0.59072 (24238) hydrogen bonds : bond 0.04198 ( 569) hydrogen bonds : angle 4.66810 ( 1707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 62 is missing expected H atoms. Skipping. Evaluate side-chains 374 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 329 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 175 GLN cc_start: 0.7489 (pm20) cc_final: 0.7138 (pm20) REVERT: B 108 LYS cc_start: 0.8077 (tptm) cc_final: 0.7782 (tttt) REVERT: F 228 GLU cc_start: 0.6828 (tp30) cc_final: 0.6467 (tp30) REVERT: I 86 GLN cc_start: 0.8215 (mm110) cc_final: 0.7917 (mm110) REVERT: I 174 ASP cc_start: 0.8459 (m-30) cc_final: 0.8113 (m-30) REVERT: I 207 MET cc_start: 0.7830 (mpp) cc_final: 0.7476 (mpp) REVERT: J 75 LYS cc_start: 0.8411 (tttm) cc_final: 0.8159 (tppt) REVERT: P 65 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8705 (tmm-80) REVERT: P 112 ASN cc_start: 0.7830 (m-40) cc_final: 0.7477 (m-40) outliers start: 45 outliers final: 32 residues processed: 357 average time/residue: 0.4570 time to fit residues: 220.9335 Evaluate side-chains 350 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 317 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain P residue 65 ARG Chi-restraints excluded: chain P residue 88 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 189 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.073161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.065347 restraints weight = 228571.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.067927 restraints weight = 91833.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.069459 restraints weight = 45837.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.070405 restraints weight = 26333.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.070991 restraints weight = 16808.563| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17920 Z= 0.157 Angle : 0.605 8.320 24238 Z= 0.325 Chirality : 0.042 0.156 2772 Planarity : 0.004 0.054 3118 Dihedral : 5.666 52.610 2456 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.58 % Allowed : 19.43 % Favored : 77.99 % 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: -1.15 (0.17), residues: 2235 helix: 0.43 (0.17), residues: 878 sheet: -1.33 (0.22), residues: 474 loop : -1.56 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 126 TYR 0.022 0.002 TYR D 156 PHE 0.021 0.002 PHE D 75 TRP 0.013 0.001 TRP D 159 HIS 0.008 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00351 (17920) covalent geometry : angle 0.60510 (24238) hydrogen bonds : bond 0.04204 ( 569) hydrogen bonds : angle 4.66189 ( 1707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 62 is missing expected H atoms. Skipping. Evaluate side-chains 366 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 317 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 175 GLN cc_start: 0.7544 (pm20) cc_final: 0.7207 (pm20) REVERT: B 108 LYS cc_start: 0.8131 (tptm) cc_final: 0.7828 (tttt) REVERT: C 109 GLU cc_start: 0.8488 (tp30) cc_final: 0.7621 (mm-30) REVERT: C 149 TYR cc_start: 0.6989 (m-80) cc_final: 0.6751 (m-80) REVERT: D 169 LYS cc_start: 0.8970 (ptmm) cc_final: 0.8754 (pptt) REVERT: I 86 GLN cc_start: 0.8111 (mm110) cc_final: 0.7844 (mm110) REVERT: I 174 ASP cc_start: 0.8442 (m-30) cc_final: 0.8100 (m-30) REVERT: I 207 MET cc_start: 0.7807 (mpp) cc_final: 0.7511 (mpp) REVERT: J 75 LYS cc_start: 0.8408 (tttm) cc_final: 0.8146 (tppt) REVERT: P 65 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8755 (tmm-80) outliers start: 49 outliers final: 40 residues processed: 346 average time/residue: 0.4561 time to fit residues: 213.5569 Evaluate side-chains 348 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 307 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain G residue 22 PHE Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain P residue 65 ARG Chi-restraints excluded: chain P residue 88 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 218 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 145 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN E 185 ASN G 73 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.073936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.066168 restraints weight = 226612.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.068747 restraints weight = 90566.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.070294 restraints weight = 44933.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.071230 restraints weight = 25623.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.071814 restraints weight = 16219.380| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17920 Z= 0.124 Angle : 0.584 8.986 24238 Z= 0.309 Chirality : 0.041 0.144 2772 Planarity : 0.004 0.065 3118 Dihedral : 5.348 49.358 2454 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.42 % Allowed : 19.33 % Favored : 78.25 % 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 (0.18), residues: 2235 helix: 0.62 (0.17), residues: 879 sheet: -1.22 (0.23), residues: 468 loop : -1.51 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 86 TYR 0.020 0.001 TYR A 155 PHE 0.022 0.001 PHE D 75 TRP 0.013 0.001 TRP D 159 HIS 0.007 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00283 (17920) covalent geometry : angle 0.58379 (24238) hydrogen bonds : bond 0.03922 ( 569) hydrogen bonds : angle 4.52088 ( 1707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 62 is missing expected H atoms. Skipping. Evaluate side-chains 360 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 314 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.7517 (pm20) cc_final: 0.7149 (pm20) REVERT: B 108 LYS cc_start: 0.8029 (tptm) cc_final: 0.7685 (tttt) REVERT: B 224 TYR cc_start: 0.7832 (p90) cc_final: 0.7604 (p90) REVERT: C 109 GLU cc_start: 0.8477 (tp30) cc_final: 0.7918 (tp30) REVERT: D 169 LYS cc_start: 0.8963 (ptmm) cc_final: 0.8752 (pptt) REVERT: I 86 GLN cc_start: 0.8171 (mm110) cc_final: 0.7770 (mm110) REVERT: I 174 ASP cc_start: 0.8409 (m-30) cc_final: 0.8063 (m-30) REVERT: I 207 MET cc_start: 0.7734 (mpp) cc_final: 0.7426 (mpp) REVERT: P 65 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8781 (tmm-80) REVERT: P 112 ASN cc_start: 0.7886 (m-40) cc_final: 0.7628 (m-40) outliers start: 46 outliers final: 35 residues processed: 340 average time/residue: 0.4575 time to fit residues: 210.3454 Evaluate side-chains 341 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 305 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain P residue 65 ARG Chi-restraints excluded: chain P residue 88 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 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 = 0.3770 r_free = 0.3770 target = 0.071665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.063978 restraints weight = 231474.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.066482 restraints weight = 93224.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.067987 restraints weight = 46752.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.068900 restraints weight = 26979.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.069471 restraints weight = 17379.852| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17920 Z= 0.212 Angle : 0.654 9.055 24238 Z= 0.354 Chirality : 0.043 0.155 2772 Planarity : 0.005 0.074 3118 Dihedral : 5.710 49.976 2454 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.26 % Allowed : 20.12 % Favored : 77.62 % 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: -1.37 (0.17), residues: 2235 helix: 0.24 (0.17), residues: 882 sheet: -1.45 (0.23), residues: 466 loop : -1.69 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 126 TYR 0.032 0.002 TYR D 156 PHE 0.023 0.002 PHE D 75 TRP 0.014 0.002 TRP B 159 HIS 0.011 0.002 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00465 (17920) covalent geometry : angle 0.65432 (24238) hydrogen bonds : bond 0.04464 ( 569) hydrogen bonds : angle 4.78290 ( 1707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 62 is missing expected H atoms. Skipping. Evaluate side-chains 355 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 312 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.7627 (pm20) cc_final: 0.7249 (pm20) REVERT: B 108 LYS cc_start: 0.8258 (tptm) cc_final: 0.7908 (tttt) REVERT: C 149 TYR cc_start: 0.6793 (m-80) cc_final: 0.6187 (m-80) REVERT: D 98 LEU cc_start: 0.7843 (tp) cc_final: 0.7560 (tt) REVERT: I 86 GLN cc_start: 0.8120 (mm110) cc_final: 0.7847 (mm110) REVERT: I 174 ASP cc_start: 0.8483 (m-30) cc_final: 0.8172 (m-30) REVERT: I 207 MET cc_start: 0.7825 (mpp) cc_final: 0.7556 (mpp) REVERT: J 75 LYS cc_start: 0.8445 (tttm) cc_final: 0.8165 (tppt) REVERT: P 65 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8778 (tmm-80) outliers start: 43 outliers final: 37 residues processed: 336 average time/residue: 0.4870 time to fit residues: 220.6605 Evaluate side-chains 341 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 15 PHE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain P residue 65 ARG Chi-restraints excluded: chain P residue 73 ARG Chi-restraints excluded: chain P residue 88 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 167 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 192 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 ASN ** 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 = 0.3774 r_free = 0.3774 target = 0.071661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.064122 restraints weight = 229607.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.066614 restraints weight = 91446.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.068112 restraints weight = 45460.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.069030 restraints weight = 25953.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.069598 restraints weight = 16414.521| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 17920 Z= 0.204 Angle : 0.817 59.200 24238 Z= 0.463 Chirality : 0.044 0.526 2772 Planarity : 0.005 0.075 3118 Dihedral : 5.693 49.975 2454 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.26 % Allowed : 20.48 % Favored : 77.25 % 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: -1.39 (0.17), residues: 2235 helix: 0.22 (0.17), residues: 882 sheet: -1.45 (0.23), residues: 469 loop : -1.70 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 128 TYR 0.030 0.002 TYR D 156 PHE 0.032 0.002 PHE K 176 TRP 0.012 0.001 TRP B 159 HIS 0.017 0.002 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00444 (17920) covalent geometry : angle 0.81739 (24238) hydrogen bonds : bond 0.04422 ( 569) hydrogen bonds : angle 4.77191 ( 1707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6373.68 seconds wall clock time: 109 minutes 35.24 seconds (6575.24 seconds total)