Starting phenix.real_space_refine on Mon Aug 25 00:46:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tsh_41592/08_2025/8tsh_41592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tsh_41592/08_2025/8tsh_41592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tsh_41592/08_2025/8tsh_41592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tsh_41592/08_2025/8tsh_41592.map" model { file = "/net/cci-nas-00/data/ceres_data/8tsh_41592/08_2025/8tsh_41592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tsh_41592/08_2025/8tsh_41592.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.862 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 100 5.16 5 C 15641 2.51 5 N 4185 2.21 5 O 4320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24254 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1708 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain: "B" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1708 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain: "C" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2062 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "D" Number of atoms: 2033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2033 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Chain: "E" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2073 Classifications: {'peptide': 255} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 246} Chain breaks: 2 Chain: "F" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2158 Classifications: {'peptide': 265} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 256} Chain breaks: 2 Chain: "G" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2140 Classifications: {'peptide': 263} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 254} Chain breaks: 2 Chain: "H" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2065 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 245} Chain breaks: 2 Chain: "I" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2032 Classifications: {'peptide': 251} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 241} Chain breaks: 2 Chain: "J" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2115 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 250} Chain breaks: 2 Chain: "K" Number of atoms: 2042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2042 Classifications: {'peptide': 251} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 242} Chain breaks: 2 Chain: "L" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2054 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 244} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.24, per 1000 atoms: 0.26 Number of scatterers: 24254 At special positions: 0 Unit cell: (130.68, 132.84, 174.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 6 15.00 Mg 2 11.99 O 4320 8.00 N 4185 7.00 C 15641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 77 " - pdb=" SG CYS L 138 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 138 " - pdb=" SG CYS I 77 " distance=2.03 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS J 77 " distance=2.03 Simple disulfide: pdb=" SG CYS K 138 " - pdb=" SG CYS L 77 " distance=1.90 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: 2.15 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 14 sheets defined 68.7% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 83 through 95 removed outlier: 3.577A pdb=" N TYR A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.883A pdb=" N PHE A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 3.931A pdb=" N VAL A 155 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 156 " --> pdb=" O MET A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 152 through 156' Processing helix chain 'A' and resid 157 through 171 Processing helix chain 'A' and resid 183 through 191 Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.731A pdb=" N GLY A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.577A pdb=" N TYR B 126 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 141 Processing helix chain 'B' and resid 157 through 171 removed outlier: 3.801A pdb=" N ARG B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 207 through 217 Processing helix chain 'C' and resid 15 through 36 removed outlier: 3.902A pdb=" N LYS C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 69 Proline residue: C 50 - end of helix removed outlier: 3.674A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ALA C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 102 removed outlier: 3.613A pdb=" N GLY C 81 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 4.509A pdb=" N ILE C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 142 removed outlier: 3.812A pdb=" N THR C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C 126 " --> pdb=" O MET C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 177 removed outlier: 3.585A pdb=" N ASN C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 181 through 188 removed outlier: 4.065A pdb=" N ILE C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 removed outlier: 3.774A pdb=" N LEU C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.851A pdb=" N THR C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 217 through 229 removed outlier: 3.603A pdb=" N HIS C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 263 Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'D' and resid 15 through 37 removed outlier: 3.879A pdb=" N LYS D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 47 through 59 removed outlier: 4.710A pdb=" N VAL D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET D 57 " --> pdb=" O HIS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 69 Processing helix chain 'D' and resid 73 through 97 removed outlier: 3.881A pdb=" N ILE D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 81 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 83 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 112 through 142 removed outlier: 3.778A pdb=" N THR D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 117 " --> pdb=" O PRO D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 176 Processing helix chain 'D' and resid 180 through 197 removed outlier: 3.837A pdb=" N ALA D 184 " --> pdb=" O PRO D 180 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 185 " --> pdb=" O GLN D 181 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Proline residue: D 192 - end of helix removed outlier: 3.652A pdb=" N PHE D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.796A pdb=" N THR D 205 " --> pdb=" O PRO D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 215 removed outlier: 3.556A pdb=" N LEU D 214 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 231 removed outlier: 3.630A pdb=" N HIS D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 263 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.657A pdb=" N LEU D 267 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 263 through 268' Processing helix chain 'E' and resid 11 through 33 removed outlier: 4.297A pdb=" N LEU E 21 " --> pdb=" O ALA E 17 " (cutoff:3.500A) Proline residue: E 22 - end of helix Processing helix chain 'E' and resid 72 through 84 removed outlier: 4.120A pdb=" N HIS E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 97 Processing helix chain 'E' and resid 97 through 103 Processing helix chain 'E' and resid 118 through 129 Processing helix chain 'E' and resid 149 through 204 removed outlier: 3.967A pdb=" N SER E 172 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET E 175 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 317 Processing helix chain 'E' and resid 340 through 368 removed outlier: 3.570A pdb=" N ASP E 368 " --> pdb=" O ALA E 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 8 Processing helix chain 'F' and resid 13 through 19 Processing helix chain 'F' and resid 19 through 33 Processing helix chain 'F' and resid 73 through 84 removed outlier: 3.812A pdb=" N CYS F 77 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS F 84 " --> pdb=" O GLN F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 97 removed outlier: 3.751A pdb=" N LYS F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 103 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 149 through 204 removed outlier: 3.698A pdb=" N GLN F 154 " --> pdb=" O PRO F 150 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET F 175 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN F 179 " --> pdb=" O MET F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 317 Processing helix chain 'F' and resid 340 through 370 Processing helix chain 'G' and resid 5 through 9 removed outlier: 3.926A pdb=" N LEU G 9 " --> pdb=" O VAL G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 19 Processing helix chain 'G' and resid 19 through 33 Processing helix chain 'G' and resid 72 through 84 removed outlier: 3.858A pdb=" N THR G 76 " --> pdb=" O SER G 72 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 97 removed outlier: 3.702A pdb=" N LYS G 91 " --> pdb=" O GLY G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 103 Processing helix chain 'G' and resid 118 through 129 Processing helix chain 'G' and resid 149 through 203 removed outlier: 3.848A pdb=" N SER G 172 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU G 178 " --> pdb=" O ARG G 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN G 179 " --> pdb=" O MET G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 319 Processing helix chain 'G' and resid 340 through 368 Processing helix chain 'H' and resid 12 through 31 removed outlier: 3.781A pdb=" N LEU H 21 " --> pdb=" O ALA H 17 " (cutoff:3.500A) Proline residue: H 22 - end of helix removed outlier: 3.560A pdb=" N LEU H 31 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 83 removed outlier: 3.748A pdb=" N THR H 76 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR H 81 " --> pdb=" O CYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 removed outlier: 3.685A pdb=" N LYS H 91 " --> pdb=" O GLY H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 103 Processing helix chain 'H' and resid 118 through 129 Processing helix chain 'H' and resid 149 through 204 removed outlier: 4.012A pdb=" N SER H 172 " --> pdb=" O VAL H 168 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET H 175 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG H 189 " --> pdb=" O ALA H 185 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU H 196 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 317 Processing helix chain 'H' and resid 340 through 369 removed outlier: 3.873A pdb=" N ALA H 346 " --> pdb=" O TRP H 342 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR H 347 " --> pdb=" O TYR H 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 33 removed outlier: 5.163A pdb=" N LEU I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) Proline residue: I 22 - end of helix Processing helix chain 'I' and resid 73 through 84 removed outlier: 3.568A pdb=" N CYS I 77 " --> pdb=" O ARG I 73 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR I 78 " --> pdb=" O GLU I 74 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU I 79 " --> pdb=" O ASP I 75 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N HIS I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 97 removed outlier: 3.560A pdb=" N LYS I 91 " --> pdb=" O GLY I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 103 Processing helix chain 'I' and resid 118 through 129 Processing helix chain 'I' and resid 149 through 202 removed outlier: 3.912A pdb=" N SER I 172 " --> pdb=" O VAL I 168 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET I 175 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 292 through 319 removed outlier: 3.629A pdb=" N PHE I 298 " --> pdb=" O LEU I 294 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU I 300 " --> pdb=" O VAL I 296 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP I 301 " --> pdb=" O GLY I 297 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR I 318 " --> pdb=" O ARG I 314 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 365 Processing helix chain 'J' and resid 11 through 19 Processing helix chain 'J' and resid 20 through 32 removed outlier: 3.878A pdb=" N VAL J 25 " --> pdb=" O LEU J 21 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA J 26 " --> pdb=" O PRO J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 84 removed outlier: 3.852A pdb=" N ASP J 75 " --> pdb=" O ALA J 71 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU J 79 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN J 80 " --> pdb=" O THR J 76 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR J 81 " --> pdb=" O CYS J 77 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS J 84 " --> pdb=" O GLN J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 97 Processing helix chain 'J' and resid 97 through 103 Processing helix chain 'J' and resid 118 through 129 Processing helix chain 'J' and resid 149 through 204 removed outlier: 3.729A pdb=" N GLN J 154 " --> pdb=" O PRO J 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER J 172 " --> pdb=" O VAL J 168 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET J 175 " --> pdb=" O LEU J 171 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG J 189 " --> pdb=" O ALA J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 317 Processing helix chain 'J' and resid 340 through 370 Processing helix chain 'K' and resid 20 through 33 Processing helix chain 'K' and resid 72 through 84 removed outlier: 4.217A pdb=" N HIS K 84 " --> pdb=" O GLN K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 97 Processing helix chain 'K' and resid 97 through 103 Processing helix chain 'K' and resid 118 through 129 Processing helix chain 'K' and resid 149 through 202 removed outlier: 3.924A pdb=" N SER K 172 " --> pdb=" O VAL K 168 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 317 removed outlier: 3.805A pdb=" N ILE K 315 " --> pdb=" O GLU K 311 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU K 316 " --> pdb=" O SER K 312 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA K 317 " --> pdb=" O ALA K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 368 Processing helix chain 'L' and resid 11 through 17 Processing helix chain 'L' and resid 19 through 33 removed outlier: 3.679A pdb=" N MET L 23 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 84 removed outlier: 4.238A pdb=" N TYR L 78 " --> pdb=" O GLU L 74 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU L 79 " --> pdb=" O ASP L 75 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS L 84 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 97 removed outlier: 3.646A pdb=" N LYS L 91 " --> pdb=" O GLY L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 103 Processing helix chain 'L' and resid 118 through 129 Processing helix chain 'L' and resid 149 through 204 removed outlier: 3.559A pdb=" N ALA L 153 " --> pdb=" O GLU L 149 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN L 154 " --> pdb=" O PRO L 150 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER L 172 " --> pdb=" O VAL L 168 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET L 175 " --> pdb=" O LEU L 171 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 317 Processing helix chain 'L' and resid 340 through 366 removed outlier: 3.650A pdb=" N ALA L 346 " --> pdb=" O TRP L 342 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR L 347 " --> pdb=" O TYR L 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.570A pdb=" N GLU A 61 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 12 removed outlier: 6.002A pdb=" N LEU A 7 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 23 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR A 11 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR A 19 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 6.435A pdb=" N ILE A 34 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLY A 35 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL A 197 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA5, first strand: chain 'B' and resid 7 through 13 removed outlier: 6.644A pdb=" N LEU B 7 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG B 22 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS B 9 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 11 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG B 18 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 73 removed outlier: 6.764A pdb=" N VAL B 72 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TYR B 147 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL B 180 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE B 149 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLY B 35 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL B 197 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 37 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 130 through 135 removed outlier: 7.137A pdb=" N THR E 45 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL E 326 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG E 47 " --> pdb=" O LEU E 324 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU E 324 " --> pdb=" O ARG E 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 131 through 135 removed outlier: 3.550A pdb=" N LEU F 140 " --> pdb=" O ASP F 135 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR F 45 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL F 326 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG F 47 " --> pdb=" O LEU F 324 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU F 324 " --> pdb=" O ARG F 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 130 through 135 removed outlier: 7.298A pdb=" N THR G 45 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL G 326 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG G 47 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU G 324 " --> pdb=" O ARG G 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 135 removed outlier: 7.320A pdb=" N THR H 45 " --> pdb=" O VAL H 326 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL H 326 " --> pdb=" O THR H 45 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG H 47 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU H 324 " --> pdb=" O ARG H 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 130 through 135 removed outlier: 6.973A pdb=" N THR I 45 " --> pdb=" O VAL I 326 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL I 326 " --> pdb=" O THR I 45 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG I 47 " --> pdb=" O LEU I 324 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU I 324 " --> pdb=" O ARG I 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 130 through 135 removed outlier: 7.188A pdb=" N THR J 45 " --> pdb=" O VAL J 326 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL J 326 " --> pdb=" O THR J 45 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG J 47 " --> pdb=" O LEU J 324 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU J 324 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 130 through 135 removed outlier: 7.004A pdb=" N THR K 45 " --> pdb=" O VAL K 326 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL K 326 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG K 47 " --> pdb=" O LEU K 324 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU K 324 " --> pdb=" O ARG K 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 130 through 135 removed outlier: 7.243A pdb=" N THR L 45 " --> pdb=" O VAL L 326 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL L 326 " --> pdb=" O THR L 45 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG L 47 " --> pdb=" O LEU L 324 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU L 324 " --> pdb=" O ARG L 47 " (cutoff:3.500A) 1611 hydrogen bonds defined for protein. 4716 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: 4.60 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7827 1.34 - 1.46: 4482 1.46 - 1.58: 12277 1.58 - 1.70: 8 1.70 - 1.82: 164 Bond restraints: 24758 Sorted by residual: bond pdb=" N THR L 76 " pdb=" CA THR L 76 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.95e+00 bond pdb=" N VAL L 25 " pdb=" CA VAL L 25 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.80e+00 bond pdb=" N VAL F 130 " pdb=" CA VAL F 130 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.27e-02 6.20e+03 7.75e+00 bond pdb=" N LEU F 133 " pdb=" CA LEU F 133 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.74e+00 bond pdb=" N VAL L 28 " pdb=" CA VAL L 28 " ideal model delta sigma weight residual 1.463 1.493 -0.030 1.14e-02 7.69e+03 7.07e+00 ... (remaining 24753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 33113 2.02 - 4.04: 363 4.04 - 6.06: 75 6.06 - 8.08: 19 8.08 - 10.10: 4 Bond angle restraints: 33574 Sorted by residual: angle pdb=" CA GLN H 181 " pdb=" CB GLN H 181 " pdb=" CG GLN H 181 " ideal model delta sigma weight residual 114.10 121.69 -7.59 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CB GLN H 181 " pdb=" CG GLN H 181 " pdb=" CD GLN H 181 " ideal model delta sigma weight residual 112.60 118.83 -6.23 1.70e+00 3.46e-01 1.34e+01 angle pdb=" CA GLU K 186 " pdb=" CB GLU K 186 " pdb=" CG GLU K 186 " ideal model delta sigma weight residual 114.10 121.17 -7.07 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CB GLU K 186 " pdb=" CG GLU K 186 " pdb=" CD GLU K 186 " ideal model delta sigma weight residual 112.60 118.41 -5.81 1.70e+00 3.46e-01 1.17e+01 angle pdb=" CB MET I 23 " pdb=" CG MET I 23 " pdb=" SD MET I 23 " ideal model delta sigma weight residual 112.70 102.60 10.10 3.00e+00 1.11e-01 1.13e+01 ... (remaining 33569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 12527 18.10 - 36.19: 1689 36.19 - 54.29: 520 54.29 - 72.39: 99 72.39 - 90.48: 44 Dihedral angle restraints: 14879 sinusoidal: 6073 harmonic: 8806 Sorted by residual: dihedral pdb=" CB CYS I 138 " pdb=" SG CYS I 138 " pdb=" SG CYS J 77 " pdb=" CB CYS J 77 " ideal model delta sinusoidal sigma weight residual 93.00 -176.52 -90.48 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CA ASP B 31 " pdb=" CB ASP B 31 " pdb=" CG ASP B 31 " pdb=" OD1 ASP B 31 " ideal model delta sinusoidal sigma weight residual -30.00 -89.09 59.09 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP B 143 " pdb=" CB ASP B 143 " pdb=" CG ASP B 143 " pdb=" OD1 ASP B 143 " ideal model delta sinusoidal sigma weight residual -30.00 -88.57 58.57 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 14876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3017 0.045 - 0.090: 603 0.090 - 0.135: 187 0.135 - 0.180: 20 0.180 - 0.225: 3 Chirality restraints: 3830 Sorted by residual: chirality pdb=" CB ILE C 54 " pdb=" CA ILE C 54 " pdb=" CG1 ILE C 54 " pdb=" CG2 ILE C 54 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA VAL L 28 " pdb=" N VAL L 28 " pdb=" C VAL L 28 " pdb=" CB VAL L 28 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CB THR C 58 " pdb=" CA THR C 58 " pdb=" OG1 THR C 58 " pdb=" CG2 THR C 58 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 3827 not shown) Planarity restraints: 4246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP L 75 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C ASP L 75 " -0.046 2.00e-02 2.50e+03 pdb=" O ASP L 75 " 0.017 2.00e-02 2.50e+03 pdb=" N THR L 76 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 129 " -0.213 9.50e-02 1.11e+02 9.57e-02 5.62e+00 pdb=" NE ARG F 129 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG F 129 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG F 129 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 129 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 186 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" CD GLU K 186 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU K 186 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU K 186 " 0.014 2.00e-02 2.50e+03 ... (remaining 4243 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 192 2.58 - 3.16: 19082 3.16 - 3.74: 39207 3.74 - 4.32: 50249 4.32 - 4.90: 85390 Nonbonded interactions: 194120 Sorted by model distance: nonbonded pdb=" OG SER B 45 " pdb="MG MG B 302 " model vdw 2.003 2.170 nonbonded pdb=" O THR C 58 " pdb=" OG SER C 62 " model vdw 2.239 3.040 nonbonded pdb=" OG SER C 167 " pdb=" OG SER C 252 " model vdw 2.247 3.040 nonbonded pdb=" O HIS J 101 " pdb=" OG1 THR J 104 " model vdw 2.248 3.040 nonbonded pdb=" O PHE L 111 " pdb=" OH TYR L 125 " model vdw 2.251 3.040 ... (remaining 194115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 14 through 268) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 13 through 50 or resid 72 through 202 or resid 291 through \ 365)) selection = (chain 'F' and (resid 13 through 202 or resid 291 through 365)) selection = (chain 'G' and (resid 13 through 50 or resid 72 through 202 or resid 291 through \ 365)) selection = (chain 'H' and (resid 13 through 50 or resid 72 through 202 or resid 291 through \ 365)) selection = (chain 'I' and (resid 13 through 50 or resid 72 through 202 or resid 291 through \ 365)) selection = (chain 'J' and (resid 13 through 50 or resid 72 through 202 or resid 291 through \ 365)) selection = (chain 'K' and (resid 13 through 50 or resid 72 through 365)) selection = (chain 'L' and (resid 13 through 50 or resid 72 through 202 or resid 291 through \ 365)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.630 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.003 0.131 24764 Z= 0.151 Angle : 0.574 17.459 33586 Z= 0.297 Chirality : 0.040 0.225 3830 Planarity : 0.004 0.096 4246 Dihedral : 18.660 89.985 9149 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.19 % Allowed : 31.02 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: 1.77 (0.16), residues: 2944 helix: 2.01 (0.12), residues: 1925 sheet: 0.91 (0.32), residues: 332 loop : -1.14 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 314 TYR 0.031 0.001 TYR E 303 PHE 0.028 0.001 PHE G 298 TRP 0.015 0.001 TRP H 16 HIS 0.003 0.000 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00280 (24758) covalent geometry : angle 0.56519 (33574) SS BOND : bond 0.05358 ( 6) SS BOND : angle 5.22543 ( 12) hydrogen bonds : bond 0.11137 ( 1611) hydrogen bonds : angle 5.04023 ( 4716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 350 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: F 135 ASP cc_start: 0.7768 (t0) cc_final: 0.7145 (t0) REVERT: G 303 TYR cc_start: 0.7180 (t80) cc_final: 0.6630 (t80) REVERT: K 181 GLN cc_start: 0.8729 (tt0) cc_final: 0.8366 (tp-100) REVERT: K 368 ASP cc_start: 0.8512 (t70) cc_final: 0.8271 (t0) REVERT: L 23 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.6756 (tpt) REVERT: L 74 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7253 (tm-30) REVERT: L 304 LYS cc_start: 0.8680 (mppt) cc_final: 0.8428 (mmtp) REVERT: L 338 TYR cc_start: 0.9400 (m-80) cc_final: 0.9188 (m-80) outliers start: 5 outliers final: 2 residues processed: 353 average time/residue: 0.1810 time to fit residues: 99.2541 Evaluate side-chains 334 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 331 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain L residue 23 MET Chi-restraints excluded: chain L residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.123910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.085583 restraints weight = 48196.444| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.53 r_work: 0.3065 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24764 Z= 0.200 Angle : 0.537 9.860 33586 Z= 0.277 Chirality : 0.040 0.195 3830 Planarity : 0.004 0.043 4246 Dihedral : 5.632 67.899 3413 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.46 % Allowed : 27.68 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: 2.02 (0.16), residues: 2944 helix: 2.15 (0.12), residues: 1971 sheet: 0.88 (0.32), residues: 332 loop : -1.04 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 129 TYR 0.018 0.001 TYR E 303 PHE 0.027 0.001 PHE G 298 TRP 0.011 0.001 TRP G 342 HIS 0.005 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00470 (24758) covalent geometry : angle 0.53680 (33574) SS BOND : bond 0.00318 ( 6) SS BOND : angle 1.49571 ( 12) hydrogen bonds : bond 0.04448 ( 1611) hydrogen bonds : angle 4.00817 ( 4716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 339 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: D 33 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8752 (tptt) REVERT: D 49 GLU cc_start: 0.8273 (tp30) cc_final: 0.8057 (tp30) REVERT: D 53 HIS cc_start: 0.8608 (m90) cc_final: 0.7729 (m90) REVERT: D 109 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7021 (ttm170) REVERT: D 153 GLU cc_start: 0.9108 (mp0) cc_final: 0.8865 (mp0) REVERT: F 134 MET cc_start: 0.8942 (ttt) cc_final: 0.8687 (ttt) REVERT: F 135 ASP cc_start: 0.8716 (t0) cc_final: 0.8301 (t0) REVERT: F 138 CYS cc_start: 0.8524 (m) cc_final: 0.8153 (m) REVERT: G 201 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.4446 (mm) REVERT: G 316 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8030 (tm-30) REVERT: H 135 ASP cc_start: 0.9154 (t0) cc_final: 0.8822 (t0) REVERT: J 135 ASP cc_start: 0.8881 (t0) cc_final: 0.8530 (t0) REVERT: J 304 LYS cc_start: 0.8892 (pptt) cc_final: 0.8684 (pptt) REVERT: J 322 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8597 (mtmt) REVERT: J 324 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8801 (tt) REVERT: K 135 ASP cc_start: 0.8761 (t0) cc_final: 0.8183 (t0) REVERT: K 181 GLN cc_start: 0.8903 (tt0) cc_final: 0.8454 (tp-100) REVERT: K 311 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7938 (tp30) REVERT: L 23 MET cc_start: 0.7852 (tmm) cc_final: 0.7260 (tpt) REVERT: L 74 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8118 (tm-30) outliers start: 115 outliers final: 61 residues processed: 428 average time/residue: 0.1804 time to fit residues: 120.7391 Evaluate side-chains 393 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 328 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 351 VAL Chi-restraints excluded: chain J residue 358 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 182 PHE Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 325 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 161 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 215 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.086900 restraints weight = 48284.878| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.54 r_work: 0.3075 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24764 Z= 0.158 Angle : 0.506 9.889 33586 Z= 0.259 Chirality : 0.039 0.160 3830 Planarity : 0.003 0.037 4246 Dihedral : 5.307 73.045 3407 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.96 % Allowed : 27.76 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: 2.12 (0.16), residues: 2944 helix: 2.25 (0.12), residues: 1971 sheet: 0.85 (0.32), residues: 332 loop : -1.01 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 314 TYR 0.014 0.001 TYR B 126 PHE 0.026 0.001 PHE G 298 TRP 0.013 0.001 TRP D 45 HIS 0.004 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00366 (24758) covalent geometry : angle 0.50532 (33574) SS BOND : bond 0.00306 ( 6) SS BOND : angle 1.81043 ( 12) hydrogen bonds : bond 0.04095 ( 1611) hydrogen bonds : angle 3.84185 ( 4716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 355 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6629 (mmt) cc_final: 0.6213 (mmm) REVERT: A 140 MET cc_start: 0.8493 (mmm) cc_final: 0.7953 (tpp) REVERT: C 14 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7705 (ttp80) REVERT: D 31 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7571 (mm-30) REVERT: D 33 LYS cc_start: 0.9023 (mmmt) cc_final: 0.8685 (tptt) REVERT: D 53 HIS cc_start: 0.8511 (m90) cc_final: 0.7658 (m90) REVERT: D 109 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6829 (ttm170) REVERT: D 153 GLU cc_start: 0.8926 (mp0) cc_final: 0.8589 (mp0) REVERT: F 134 MET cc_start: 0.8720 (ttt) cc_final: 0.8393 (ttt) REVERT: F 135 ASP cc_start: 0.8620 (t0) cc_final: 0.8175 (t0) REVERT: F 138 CYS cc_start: 0.8357 (m) cc_final: 0.8035 (m) REVERT: F 322 LYS cc_start: 0.8651 (mtmt) cc_final: 0.7964 (mttm) REVERT: G 316 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7984 (tm-30) REVERT: I 322 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8536 (mtpp) REVERT: J 304 LYS cc_start: 0.8960 (pptt) cc_final: 0.8741 (pptt) REVERT: J 322 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8250 (mtmt) REVERT: K 23 MET cc_start: 0.8976 (tpp) cc_final: 0.8533 (tpt) REVERT: K 135 ASP cc_start: 0.8684 (t0) cc_final: 0.8169 (t0) REVERT: K 311 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: L 23 MET cc_start: 0.7682 (tmm) cc_final: 0.7139 (tpt) REVERT: L 74 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7263 (tm-30) REVERT: L 78 TYR cc_start: 0.7956 (m-10) cc_final: 0.7433 (m-10) outliers start: 102 outliers final: 68 residues processed: 430 average time/residue: 0.1769 time to fit residues: 119.8161 Evaluate side-chains 405 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 334 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 358 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 182 PHE Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 360 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 110 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 195 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 255 optimal weight: 0.8980 chunk 245 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.124568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087397 restraints weight = 47680.945| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.48 r_work: 0.3078 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24764 Z= 0.152 Angle : 0.508 8.224 33586 Z= 0.258 Chirality : 0.039 0.194 3830 Planarity : 0.003 0.035 4246 Dihedral : 5.243 75.731 3407 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.32 % Allowed : 26.82 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: 2.19 (0.16), residues: 2944 helix: 2.31 (0.12), residues: 1973 sheet: 0.84 (0.32), residues: 330 loop : -1.02 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 314 TYR 0.020 0.001 TYR E 303 PHE 0.026 0.001 PHE G 298 TRP 0.013 0.001 TRP H 16 HIS 0.004 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00354 (24758) covalent geometry : angle 0.50704 (33574) SS BOND : bond 0.00332 ( 6) SS BOND : angle 1.59363 ( 12) hydrogen bonds : bond 0.03983 ( 1611) hydrogen bonds : angle 3.76541 ( 4716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 349 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6626 (mmt) cc_final: 0.6192 (mmm) REVERT: A 140 MET cc_start: 0.8505 (mmm) cc_final: 0.7994 (tpp) REVERT: B 177 MET cc_start: 0.8130 (tpt) cc_final: 0.7914 (tpt) REVERT: C 14 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7651 (ttp80) REVERT: D 31 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7577 (mm-30) REVERT: D 33 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8680 (tptt) REVERT: D 49 GLU cc_start: 0.8657 (tp30) cc_final: 0.8290 (tp30) REVERT: D 53 HIS cc_start: 0.8617 (m90) cc_final: 0.7687 (m90) REVERT: D 109 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6799 (ttm170) REVERT: D 132 TYR cc_start: 0.8757 (t80) cc_final: 0.8534 (t80) REVERT: D 153 GLU cc_start: 0.8912 (mp0) cc_final: 0.8551 (mp0) REVERT: F 134 MET cc_start: 0.8746 (ttt) cc_final: 0.8402 (ttt) REVERT: F 135 ASP cc_start: 0.8599 (t0) cc_final: 0.8158 (t0) REVERT: F 138 CYS cc_start: 0.8407 (m) cc_final: 0.8132 (m) REVERT: F 322 LYS cc_start: 0.8640 (mtmt) cc_final: 0.7980 (mttm) REVERT: G 201 LEU cc_start: 0.4928 (OUTLIER) cc_final: 0.4495 (mm) REVERT: G 316 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8088 (tm-30) REVERT: H 23 MET cc_start: 0.7195 (mmm) cc_final: 0.6973 (mmt) REVERT: J 304 LYS cc_start: 0.8968 (pptt) cc_final: 0.8743 (pptt) REVERT: J 322 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8449 (mtmt) REVERT: J 324 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8738 (tt) REVERT: K 23 MET cc_start: 0.8950 (tpp) cc_final: 0.8441 (tpt) REVERT: K 135 ASP cc_start: 0.8682 (t0) cc_final: 0.8171 (t0) REVERT: K 311 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: K 368 ASP cc_start: 0.8573 (t70) cc_final: 0.8280 (t0) REVERT: L 23 MET cc_start: 0.7627 (tmm) cc_final: 0.7205 (tpt) REVERT: L 74 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7365 (tm-30) REVERT: L 78 TYR cc_start: 0.8241 (m-10) cc_final: 0.7723 (m-10) outliers start: 137 outliers final: 98 residues processed: 455 average time/residue: 0.1739 time to fit residues: 125.1306 Evaluate side-chains 440 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 337 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 289 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 292 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 351 VAL Chi-restraints excluded: chain J residue 358 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 182 PHE Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 315 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 360 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 269 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 279 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.124231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.087033 restraints weight = 47648.017| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.47 r_work: 0.3074 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24764 Z= 0.164 Angle : 0.515 8.157 33586 Z= 0.261 Chirality : 0.039 0.176 3830 Planarity : 0.003 0.035 4246 Dihedral : 5.127 79.045 3407 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.32 % Allowed : 27.33 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: 2.19 (0.16), residues: 2944 helix: 2.33 (0.12), residues: 1970 sheet: 0.83 (0.32), residues: 330 loop : -1.07 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 314 TYR 0.019 0.001 TYR B 126 PHE 0.027 0.001 PHE G 298 TRP 0.014 0.001 TRP H 16 HIS 0.004 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00385 (24758) covalent geometry : angle 0.51385 (33574) SS BOND : bond 0.00335 ( 6) SS BOND : angle 1.62054 ( 12) hydrogen bonds : bond 0.04030 ( 1611) hydrogen bonds : angle 3.75624 ( 4716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 345 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6653 (mmt) cc_final: 0.6289 (mmm) REVERT: A 140 MET cc_start: 0.8510 (mmm) cc_final: 0.8017 (tpp) REVERT: B 177 MET cc_start: 0.8133 (tpt) cc_final: 0.7857 (tpt) REVERT: C 14 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7549 (ttp80) REVERT: D 33 LYS cc_start: 0.9037 (mmmt) cc_final: 0.8710 (tptt) REVERT: D 53 HIS cc_start: 0.8677 (m90) cc_final: 0.7948 (m-70) REVERT: D 109 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6804 (ttm170) REVERT: D 153 GLU cc_start: 0.8944 (mp0) cc_final: 0.8574 (mp0) REVERT: F 134 MET cc_start: 0.8776 (ttt) cc_final: 0.8431 (ttt) REVERT: F 135 ASP cc_start: 0.8592 (t0) cc_final: 0.8130 (t0) REVERT: F 138 CYS cc_start: 0.8392 (m) cc_final: 0.8180 (m) REVERT: F 322 LYS cc_start: 0.8656 (mtmt) cc_final: 0.7991 (mttm) REVERT: G 201 LEU cc_start: 0.4931 (OUTLIER) cc_final: 0.4483 (mm) REVERT: G 316 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8117 (tm-30) REVERT: I 322 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8544 (mtpp) REVERT: J 301 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7694 (p0) REVERT: J 322 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8481 (mtmt) REVERT: J 324 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8764 (tt) REVERT: K 23 MET cc_start: 0.8934 (tpp) cc_final: 0.8393 (tpt) REVERT: K 135 ASP cc_start: 0.8703 (t0) cc_final: 0.8210 (t0) REVERT: K 311 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7901 (tp30) REVERT: K 368 ASP cc_start: 0.8605 (t70) cc_final: 0.8321 (t0) REVERT: L 23 MET cc_start: 0.7624 (tmm) cc_final: 0.7249 (tpt) outliers start: 137 outliers final: 112 residues processed: 452 average time/residue: 0.1757 time to fit residues: 125.9504 Evaluate side-chains 449 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 331 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 289 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 292 LEU Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain J residue 323 SER Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 351 VAL Chi-restraints excluded: chain J residue 358 VAL Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 182 PHE Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 315 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 360 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 226 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 239 optimal weight: 7.9990 chunk 14 optimal weight: 0.2980 chunk 214 optimal weight: 8.9990 chunk 275 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.125794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.089191 restraints weight = 47391.705| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.42 r_work: 0.3117 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24764 Z= 0.110 Angle : 0.492 8.367 33586 Z= 0.249 Chirality : 0.038 0.182 3830 Planarity : 0.003 0.060 4246 Dihedral : 4.934 88.015 3407 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.11 % Allowed : 28.73 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: 2.34 (0.16), residues: 2944 helix: 2.42 (0.12), residues: 1970 sheet: 0.95 (0.32), residues: 326 loop : -0.95 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 314 TYR 0.021 0.001 TYR E 303 PHE 0.028 0.001 PHE G 298 TRP 0.017 0.001 TRP D 45 HIS 0.004 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00241 (24758) covalent geometry : angle 0.49136 (33574) SS BOND : bond 0.00246 ( 6) SS BOND : angle 1.28745 ( 12) hydrogen bonds : bond 0.03642 ( 1611) hydrogen bonds : angle 3.65170 ( 4716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 358 time to evaluate : 0.908 Fit side-chains REVERT: A 1 MET cc_start: 0.6977 (mmt) cc_final: 0.6412 (mmm) REVERT: B 177 MET cc_start: 0.8158 (tpt) cc_final: 0.7855 (tpt) REVERT: C 14 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7589 (ttp80) REVERT: D 33 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8711 (tptt) REVERT: D 49 GLU cc_start: 0.8474 (tp30) cc_final: 0.8267 (tp30) REVERT: D 53 HIS cc_start: 0.8666 (m90) cc_final: 0.7945 (m-70) REVERT: D 109 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6910 (ttm170) REVERT: D 153 GLU cc_start: 0.9005 (mp0) cc_final: 0.8667 (mp0) REVERT: F 135 ASP cc_start: 0.8728 (t0) cc_final: 0.8172 (t0) REVERT: F 138 CYS cc_start: 0.8674 (m) cc_final: 0.8455 (m) REVERT: F 322 LYS cc_start: 0.8601 (mtmt) cc_final: 0.7903 (mttm) REVERT: G 201 LEU cc_start: 0.4982 (OUTLIER) cc_final: 0.4513 (mm) REVERT: G 316 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8013 (tm-30) REVERT: I 298 PHE cc_start: 0.7080 (p90) cc_final: 0.6512 (p90) REVERT: I 322 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8540 (mtpp) REVERT: J 322 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8460 (mtmt) REVERT: K 23 MET cc_start: 0.8934 (tpp) cc_final: 0.8346 (tpt) REVERT: K 135 ASP cc_start: 0.8757 (t0) cc_final: 0.8182 (t0) REVERT: K 311 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7953 (tp30) REVERT: K 368 ASP cc_start: 0.8795 (t70) cc_final: 0.8485 (t0) REVERT: L 23 MET cc_start: 0.7644 (tmm) cc_final: 0.7107 (tpt) REVERT: L 74 GLU cc_start: 0.8603 (tm-30) cc_final: 0.7349 (tm-30) REVERT: L 78 TYR cc_start: 0.8681 (m-10) cc_final: 0.8213 (m-10) REVERT: L 322 LYS cc_start: 0.9163 (mtpp) cc_final: 0.8938 (mtpp) outliers start: 106 outliers final: 80 residues processed: 436 average time/residue: 0.1689 time to fit residues: 116.1274 Evaluate side-chains 428 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 344 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 323 SER Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 182 PHE Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 315 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 154 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 253 optimal weight: 0.0570 chunk 175 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 140 optimal weight: 0.0970 chunk 231 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.125555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.088568 restraints weight = 47562.297| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.44 r_work: 0.3116 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24764 Z= 0.115 Angle : 0.502 8.662 33586 Z= 0.253 Chirality : 0.038 0.208 3830 Planarity : 0.003 0.034 4246 Dihedral : 4.817 88.999 3407 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.50 % Allowed : 28.38 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: 2.35 (0.16), residues: 2944 helix: 2.44 (0.12), residues: 1970 sheet: 0.95 (0.32), residues: 326 loop : -0.97 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 314 TYR 0.016 0.001 TYR B 126 PHE 0.028 0.001 PHE G 298 TRP 0.017 0.001 TRP D 45 HIS 0.004 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00257 (24758) covalent geometry : angle 0.50173 (33574) SS BOND : bond 0.00204 ( 6) SS BOND : angle 1.22557 ( 12) hydrogen bonds : bond 0.03587 ( 1611) hydrogen bonds : angle 3.62371 ( 4716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 355 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7020 (mmt) cc_final: 0.6418 (mmm) REVERT: B 177 MET cc_start: 0.8141 (tpt) cc_final: 0.7796 (tpt) REVERT: C 14 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7582 (ttp80) REVERT: D 33 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8746 (tptt) REVERT: D 49 GLU cc_start: 0.8415 (tp30) cc_final: 0.8086 (tp30) REVERT: D 53 HIS cc_start: 0.8610 (m90) cc_final: 0.7664 (m90) REVERT: D 109 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.6911 (ttm170) REVERT: D 153 GLU cc_start: 0.8974 (mp0) cc_final: 0.8654 (mp0) REVERT: E 340 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8289 (mtp180) REVERT: F 135 ASP cc_start: 0.8744 (t0) cc_final: 0.8244 (t0) REVERT: F 138 CYS cc_start: 0.8710 (m) cc_final: 0.8505 (m) REVERT: F 322 LYS cc_start: 0.8612 (mtmt) cc_final: 0.7934 (mttm) REVERT: G 201 LEU cc_start: 0.4907 (OUTLIER) cc_final: 0.4440 (mm) REVERT: G 316 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8020 (tm-30) REVERT: I 298 PHE cc_start: 0.7086 (p90) cc_final: 0.6514 (p90) REVERT: I 322 LYS cc_start: 0.8895 (mtmt) cc_final: 0.8533 (mtpp) REVERT: J 75 ASP cc_start: 0.8280 (m-30) cc_final: 0.7931 (t0) REVERT: J 322 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8280 (mtmt) REVERT: K 23 MET cc_start: 0.8931 (tpp) cc_final: 0.8334 (tpt) REVERT: K 135 ASP cc_start: 0.8764 (t0) cc_final: 0.8187 (t0) REVERT: K 311 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: K 368 ASP cc_start: 0.8693 (t70) cc_final: 0.8431 (t0) REVERT: L 23 MET cc_start: 0.7654 (tmm) cc_final: 0.7116 (tpt) REVERT: L 74 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8155 (tm-30) REVERT: L 184 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8194 (pp20) outliers start: 116 outliers final: 94 residues processed: 443 average time/residue: 0.1491 time to fit residues: 104.5201 Evaluate side-chains 445 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 346 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 289 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 323 SER Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 182 PHE Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 315 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 270 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 276 optimal weight: 0.7980 chunk 226 optimal weight: 0.5980 chunk 283 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.124376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.086512 restraints weight = 47952.940| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.51 r_work: 0.3068 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24764 Z= 0.189 Angle : 0.547 11.809 33586 Z= 0.276 Chirality : 0.040 0.193 3830 Planarity : 0.003 0.034 4246 Dihedral : 4.870 86.019 3407 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.74 % Allowed : 28.11 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: 2.18 (0.16), residues: 2944 helix: 2.33 (0.12), residues: 1972 sheet: 0.79 (0.32), residues: 328 loop : -1.06 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 314 TYR 0.021 0.001 TYR E 303 PHE 0.028 0.001 PHE G 298 TRP 0.015 0.001 TRP H 16 HIS 0.004 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00447 (24758) covalent geometry : angle 0.54619 (33574) SS BOND : bond 0.00270 ( 6) SS BOND : angle 1.69207 ( 12) hydrogen bonds : bond 0.04071 ( 1611) hydrogen bonds : angle 3.73335 ( 4716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 352 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7144 (mmt) cc_final: 0.6655 (mmm) REVERT: A 216 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7632 (mt0) REVERT: B 177 MET cc_start: 0.8180 (tpt) cc_final: 0.7905 (tpt) REVERT: B 183 ASN cc_start: 0.8458 (t0) cc_final: 0.8047 (t0) REVERT: C 14 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7562 (ttp80) REVERT: D 33 LYS cc_start: 0.9042 (mmmt) cc_final: 0.8710 (tptt) REVERT: D 49 GLU cc_start: 0.8643 (tp30) cc_final: 0.8293 (tp30) REVERT: D 53 HIS cc_start: 0.8637 (m90) cc_final: 0.7732 (m90) REVERT: D 109 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6960 (ttm170) REVERT: D 153 GLU cc_start: 0.9045 (mp0) cc_final: 0.8653 (mp0) REVERT: E 340 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8265 (mtp180) REVERT: F 14 LEU cc_start: 0.8811 (tp) cc_final: 0.8586 (tt) REVERT: F 135 ASP cc_start: 0.8756 (t0) cc_final: 0.8233 (t0) REVERT: F 322 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8034 (mttm) REVERT: G 316 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8030 (tm-30) REVERT: I 322 LYS cc_start: 0.8975 (mtmt) cc_final: 0.8703 (mttp) REVERT: J 322 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8494 (mtmt) REVERT: J 324 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8837 (tt) REVERT: K 23 MET cc_start: 0.9021 (tpp) cc_final: 0.8516 (tpt) REVERT: K 135 ASP cc_start: 0.8786 (t0) cc_final: 0.8238 (t0) REVERT: K 311 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: L 23 MET cc_start: 0.7803 (tmm) cc_final: 0.7171 (tpt) REVERT: L 74 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8090 (tm-30) outliers start: 122 outliers final: 106 residues processed: 446 average time/residue: 0.1356 time to fit residues: 96.8086 Evaluate side-chains 454 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 343 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 289 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 323 SER Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 358 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 182 PHE Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 315 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.125866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.089307 restraints weight = 47410.876| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.41 r_work: 0.3118 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24764 Z= 0.115 Angle : 0.517 10.027 33586 Z= 0.259 Chirality : 0.039 0.199 3830 Planarity : 0.003 0.034 4246 Dihedral : 4.716 84.446 3407 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.04 % Allowed : 28.92 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: 2.29 (0.16), residues: 2944 helix: 2.40 (0.12), residues: 1969 sheet: 0.95 (0.33), residues: 324 loop : -1.02 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 189 TYR 0.016 0.001 TYR F 356 PHE 0.028 0.001 PHE G 298 TRP 0.016 0.001 TRP H 16 HIS 0.004 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00258 (24758) covalent geometry : angle 0.51614 (33574) SS BOND : bond 0.00221 ( 6) SS BOND : angle 1.16737 ( 12) hydrogen bonds : bond 0.03611 ( 1611) hydrogen bonds : angle 3.62574 ( 4716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 356 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6989 (mmt) cc_final: 0.6438 (mmm) REVERT: A 216 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7587 (mt0) REVERT: B 1 MET cc_start: 0.6255 (tpp) cc_final: 0.6009 (tpt) REVERT: B 102 MET cc_start: 0.8728 (ttp) cc_final: 0.8482 (ttp) REVERT: B 177 MET cc_start: 0.8173 (tpt) cc_final: 0.7837 (tpt) REVERT: C 14 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7597 (ttp80) REVERT: D 33 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8749 (tptt) REVERT: D 49 GLU cc_start: 0.8498 (tp30) cc_final: 0.8056 (tp30) REVERT: D 53 HIS cc_start: 0.8610 (m90) cc_final: 0.7726 (m90) REVERT: D 109 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6899 (ttm170) REVERT: D 153 GLU cc_start: 0.8974 (mp0) cc_final: 0.8655 (mp0) REVERT: E 303 TYR cc_start: 0.7646 (t80) cc_final: 0.7438 (t80) REVERT: E 340 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8333 (mtp180) REVERT: F 135 ASP cc_start: 0.8852 (t0) cc_final: 0.8190 (t0) REVERT: F 138 CYS cc_start: 0.8052 (m) cc_final: 0.7319 (m) REVERT: F 322 LYS cc_start: 0.8629 (mtmt) cc_final: 0.7942 (mttm) REVERT: G 135 ASP cc_start: 0.8696 (t0) cc_final: 0.8257 (t0) REVERT: G 316 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8105 (tm-30) REVERT: I 298 PHE cc_start: 0.6606 (p90) cc_final: 0.6115 (p90) REVERT: I 322 LYS cc_start: 0.8866 (mtmt) cc_final: 0.8515 (mtpp) REVERT: J 75 ASP cc_start: 0.8369 (m-30) cc_final: 0.7974 (t0) REVERT: J 134 MET cc_start: 0.9226 (ttt) cc_final: 0.8674 (ttt) REVERT: J 322 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8286 (mtmt) REVERT: K 23 MET cc_start: 0.8941 (tpp) cc_final: 0.8345 (tpt) REVERT: K 135 ASP cc_start: 0.8798 (t0) cc_final: 0.8230 (t0) REVERT: K 181 GLN cc_start: 0.8753 (tt0) cc_final: 0.8359 (tp-100) REVERT: K 311 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: L 23 MET cc_start: 0.7771 (tmm) cc_final: 0.7132 (tpt) REVERT: L 74 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8310 (tm-30) REVERT: L 184 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8554 (pp20) outliers start: 104 outliers final: 90 residues processed: 439 average time/residue: 0.1638 time to fit residues: 113.0840 Evaluate side-chains 438 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 344 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 289 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 182 PHE Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 323 SER Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 182 PHE Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 315 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 360 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 110 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 247 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 115 optimal weight: 1.9990 chunk 177 optimal weight: 0.1980 chunk 192 optimal weight: 6.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.125276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.088442 restraints weight = 47576.909| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.42 r_work: 0.3105 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24764 Z= 0.136 Angle : 0.535 10.127 33586 Z= 0.267 Chirality : 0.039 0.266 3830 Planarity : 0.003 0.034 4246 Dihedral : 4.728 85.370 3407 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.00 % Allowed : 28.96 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: 2.24 (0.16), residues: 2944 helix: 2.36 (0.12), residues: 1970 sheet: 0.92 (0.32), residues: 326 loop : -1.06 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 314 TYR 0.014 0.001 TYR G 303 PHE 0.028 0.001 PHE G 298 TRP 0.026 0.001 TRP D 45 HIS 0.004 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00315 (24758) covalent geometry : angle 0.53466 (33574) SS BOND : bond 0.00233 ( 6) SS BOND : angle 1.50831 ( 12) hydrogen bonds : bond 0.03742 ( 1611) hydrogen bonds : angle 3.65265 ( 4716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 349 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7051 (mmt) cc_final: 0.6463 (mmm) REVERT: A 216 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7594 (mt0) REVERT: B 1 MET cc_start: 0.6266 (tpp) cc_final: 0.6045 (tpt) REVERT: B 102 MET cc_start: 0.8708 (ttp) cc_final: 0.8496 (ttp) REVERT: B 177 MET cc_start: 0.8231 (tpt) cc_final: 0.7877 (tpt) REVERT: C 14 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7546 (ttp80) REVERT: C 33 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8310 (mmmt) REVERT: D 33 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8753 (tptt) REVERT: D 49 GLU cc_start: 0.8442 (tp30) cc_final: 0.8058 (tp30) REVERT: D 53 HIS cc_start: 0.8599 (m90) cc_final: 0.7719 (m90) REVERT: D 109 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6893 (ttm170) REVERT: D 153 GLU cc_start: 0.8980 (mp0) cc_final: 0.8639 (mp0) REVERT: E 340 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8287 (mtp180) REVERT: F 135 ASP cc_start: 0.8765 (t0) cc_final: 0.7982 (t0) REVERT: F 138 CYS cc_start: 0.8005 (m) cc_final: 0.7160 (m) REVERT: F 322 LYS cc_start: 0.8646 (mtmt) cc_final: 0.7960 (mttm) REVERT: G 201 LEU cc_start: 0.4999 (OUTLIER) cc_final: 0.4559 (mm) REVERT: G 316 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8163 (tm-30) REVERT: I 23 MET cc_start: 0.8537 (mmm) cc_final: 0.8247 (mmm) REVERT: I 322 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8537 (mtpp) REVERT: J 75 ASP cc_start: 0.8400 (m-30) cc_final: 0.7994 (t0) REVERT: J 322 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8277 (mtmt) REVERT: K 23 MET cc_start: 0.8960 (tpp) cc_final: 0.8375 (tpt) REVERT: K 135 ASP cc_start: 0.8777 (t0) cc_final: 0.8201 (t0) REVERT: K 181 GLN cc_start: 0.8765 (tt0) cc_final: 0.8362 (tp-100) REVERT: K 311 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7933 (tp30) REVERT: L 23 MET cc_start: 0.7759 (tmm) cc_final: 0.7143 (tpt) REVERT: L 86 MET cc_start: 0.9112 (tpt) cc_final: 0.8911 (tpt) REVERT: L 184 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8569 (pp20) outliers start: 103 outliers final: 95 residues processed: 435 average time/residue: 0.1479 time to fit residues: 102.3129 Evaluate side-chains 447 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 347 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 289 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 182 PHE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 77 CYS Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 323 SER Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 182 PHE Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 315 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 242 optimal weight: 3.9990 chunk 186 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.123202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.084677 restraints weight = 48133.600| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.54 r_work: 0.3049 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24764 Z= 0.230 Angle : 0.595 9.787 33586 Z= 0.299 Chirality : 0.042 0.272 3830 Planarity : 0.004 0.035 4246 Dihedral : 4.967 85.083 3407 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.43 % Allowed : 28.77 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 aren not related in a simple way. whole: 2.05 (0.16), residues: 2944 helix: 2.24 (0.12), residues: 1970 sheet: 0.81 (0.32), residues: 328 loop : -1.16 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 22 TYR 0.027 0.002 TYR A 19 PHE 0.028 0.001 PHE G 298 TRP 0.022 0.001 TRP D 45 HIS 0.005 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00547 (24758) covalent geometry : angle 0.59360 (33574) SS BOND : bond 0.00313 ( 6) SS BOND : angle 2.07527 ( 12) hydrogen bonds : bond 0.04318 ( 1611) hydrogen bonds : angle 3.81547 ( 4716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8238.66 seconds wall clock time: 140 minutes 58.70 seconds (8458.70 seconds total)