Starting phenix.real_space_refine on Fri Jun 20 21:37:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tsh_41592/06_2025/8tsh_41592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tsh_41592/06_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_41592/06_2025/8tsh_41592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tsh_41592/06_2025/8tsh_41592.map" model { file = "/net/cci-nas-00/data/ceres_data/8tsh_41592/06_2025/8tsh_41592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tsh_41592/06_2025/8tsh_41592.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.91, per 1000 atoms: 0.74 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: 6.74 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 2.65 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: 9.87 Time building geometry restraints manager: 7.99 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: 4.550 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: 0.090 Extract box with map and model: 1.220 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 61.690 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.210 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: 0.030 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.130 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (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 TRP 0.015 0.001 TRP H 16 HIS 0.003 0.000 HIS C 204 PHE 0.028 0.001 PHE G 298 TYR 0.031 0.001 TYR E 303 ARG 0.009 0.000 ARG K 314 Details of bonding type rmsd hydrogen bonds : bond 0.11137 ( 1611) hydrogen bonds : angle 5.04023 ( 4716) SS BOND : bond 0.05358 ( 6) SS BOND : angle 5.22543 ( 12) covalent geometry : bond 0.00280 (24758) covalent geometry : angle 0.56519 (33574) *********************** 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 : 2.918 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: 0.6631 (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: 0.8420 (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: 0.3759 time to fit residues: 205.4250 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 : 2.884 ------------------------------------------------------------------------------- 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 249 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 231 optimal weight: 0.0770 chunk 89 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 172 optimal weight: 0.5980 chunk 267 optimal weight: 4.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.126036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088223 restraints weight = 48120.035| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.54 r_work: 0.3104 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24764 Z= 0.132 Angle : 0.494 7.471 33586 Z= 0.255 Chirality : 0.038 0.194 3830 Planarity : 0.003 0.043 4246 Dihedral : 5.630 69.772 3413 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.34 % Allowed : 28.14 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.16), residues: 2944 helix: 2.23 (0.12), residues: 1978 sheet: 0.91 (0.33), residues: 332 loop : -1.02 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 16 HIS 0.007 0.001 HIS F 101 PHE 0.027 0.001 PHE G 298 TYR 0.020 0.001 TYR E 303 ARG 0.005 0.000 ARG F 129 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 1611) hydrogen bonds : angle 3.93068 ( 4716) SS BOND : bond 0.00165 ( 6) SS BOND : angle 1.08136 ( 12) covalent geometry : bond 0.00296 (24758) covalent geometry : angle 0.49380 (33574) *********************** 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 437 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 351 time to evaluate : 3.066 Fit side-chains REVERT: B 1 MET cc_start: 0.6087 (tpp) cc_final: 0.5769 (tpt) REVERT: D 33 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8740 (tptt) REVERT: D 49 GLU cc_start: 0.8264 (tp30) cc_final: 0.8054 (tp30) REVERT: D 53 HIS cc_start: 0.8559 (m90) cc_final: 0.7684 (m90) REVERT: D 109 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6838 (ttm170) REVERT: D 153 GLU cc_start: 0.8976 (mp0) cc_final: 0.8754 (mp0) REVERT: F 134 MET cc_start: 0.8604 (ttt) cc_final: 0.8355 (ttt) REVERT: F 135 ASP cc_start: 0.8472 (t0) cc_final: 0.8051 (t0) REVERT: G 201 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.4476 (mm) REVERT: G 316 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8054 (tm-30) REVERT: J 135 ASP cc_start: 0.8751 (t0) cc_final: 0.8409 (t0) REVERT: J 304 LYS cc_start: 0.8887 (pptt) cc_final: 0.8680 (pptt) REVERT: K 181 GLN cc_start: 0.8860 (tt0) cc_final: 0.8426 (tp-100) REVERT: L 23 MET cc_start: 0.7833 (tmm) cc_final: 0.7237 (tpt) REVERT: L 74 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7892 (tm-30) REVERT: L 86 MET cc_start: 0.8984 (tpp) cc_final: 0.8784 (tpt) REVERT: L 338 TYR cc_start: 0.9431 (m-80) cc_final: 0.9091 (m-80) outliers start: 86 outliers final: 43 residues processed: 414 average time/residue: 0.3548 time to fit residues: 230.3065 Evaluate side-chains 383 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 338 time to evaluate : 2.723 ------------------------------------------------------------------------------- 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 180 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 HIS 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 199 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 E residue 14 LEU Chi-restraints excluded: chain E residue 320 LYS 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 365 THR Chi-restraints excluded: chain G residue 34 SER 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 137 ILE Chi-restraints excluded: chain H residue 331 VAL 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 133 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 201 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 182 PHE Chi-restraints excluded: chain K residue 307 LEU 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 260 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.121378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.082651 restraints weight = 48136.364| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.53 r_work: 0.3013 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 24764 Z= 0.348 Angle : 0.648 10.141 33586 Z= 0.333 Chirality : 0.045 0.185 3830 Planarity : 0.004 0.044 4246 Dihedral : 5.525 69.303 3407 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.78 % Allowed : 25.97 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.16), residues: 2944 helix: 1.95 (0.12), residues: 1967 sheet: 0.78 (0.32), residues: 332 loop : -1.20 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 342 HIS 0.006 0.001 HIS L 101 PHE 0.026 0.002 PHE G 298 TYR 0.020 0.002 TYR B 126 ARG 0.004 0.001 ARG F 129 Details of bonding type rmsd hydrogen bonds : bond 0.05147 ( 1611) hydrogen bonds : angle 4.13701 ( 4716) SS BOND : bond 0.00883 ( 6) SS BOND : angle 2.60256 ( 12) covalent geometry : bond 0.00823 (24758) covalent geometry : angle 0.64608 (33574) *********************** 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 497 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 348 time to evaluate : 2.696 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6781 (mmt) cc_final: 0.6455 (mmm) REVERT: C 14 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7753 (ttp80) REVERT: D 31 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7709 (mm-30) REVERT: D 33 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8727 (tptt) REVERT: D 49 GLU cc_start: 0.8583 (tp30) cc_final: 0.7969 (tp30) REVERT: D 53 HIS cc_start: 0.8622 (m90) cc_final: 0.7595 (m90) REVERT: D 78 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9101 (mp) REVERT: D 153 GLU cc_start: 0.9018 (mp0) cc_final: 0.8670 (mp0) REVERT: F 134 MET cc_start: 0.8872 (ttt) cc_final: 0.8553 (ttt) REVERT: F 135 ASP cc_start: 0.8690 (t0) cc_final: 0.8224 (t0) REVERT: F 138 CYS cc_start: 0.8348 (m) cc_final: 0.8058 (m) REVERT: F 322 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8039 (mttm) REVERT: H 23 MET cc_start: 0.7310 (mmm) cc_final: 0.7092 (mmt) REVERT: J 304 LYS cc_start: 0.8952 (pptt) cc_final: 0.8728 (pptt) REVERT: J 322 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8353 (mtmt) REVERT: J 324 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8896 (tt) REVERT: J 340 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6147 (mmm160) REVERT: K 135 ASP cc_start: 0.8710 (t0) cc_final: 0.8208 (t0) REVERT: K 311 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7970 (tp30) REVERT: L 23 MET cc_start: 0.7809 (tmm) cc_final: 0.7292 (tpt) REVERT: L 74 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7410 (tm-30) REVERT: L 78 TYR cc_start: 0.8409 (m-10) cc_final: 0.7889 (m-10) REVERT: L 324 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9061 (tt) outliers start: 149 outliers final: 97 residues processed: 464 average time/residue: 0.3541 time to fit residues: 257.0956 Evaluate side-chains 435 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 332 time to evaluate : 2.917 ------------------------------------------------------------------------------- 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 203 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 187 ILE 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 164 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 96 MET 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 171 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 131 GLU 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 331 VAL Chi-restraints excluded: chain F residue 351 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 34 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 296 VAL 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 168 VAL 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 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 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 324 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 340 ARG 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 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 142 THR Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 324 LEU 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 150 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 173 optimal weight: 0.4980 chunk 222 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.124698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087718 restraints weight = 47965.368| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.43 r_work: 0.3092 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24764 Z= 0.121 Angle : 0.503 8.556 33586 Z= 0.256 Chirality : 0.038 0.176 3830 Planarity : 0.003 0.036 4246 Dihedral : 5.254 77.373 3407 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.42 % Allowed : 29.08 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.16), residues: 2944 helix: 2.25 (0.12), residues: 1971 sheet: 0.80 (0.32), residues: 330 loop : -1.08 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 342 HIS 0.006 0.001 HIS F 101 PHE 0.027 0.001 PHE G 298 TYR 0.014 0.001 TYR B 126 ARG 0.005 0.000 ARG K 314 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 1611) hydrogen bonds : angle 3.80262 ( 4716) SS BOND : bond 0.00325 ( 6) SS BOND : angle 1.27329 ( 12) covalent geometry : bond 0.00268 (24758) covalent geometry : angle 0.50239 (33574) *********************** 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 442 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 354 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6628 (mmt) cc_final: 0.6191 (mmm) REVERT: A 140 MET cc_start: 0.8417 (mmm) cc_final: 0.7955 (tpp) REVERT: B 177 MET cc_start: 0.8010 (tpt) cc_final: 0.7807 (tpt) REVERT: C 14 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7635 (ttp80) REVERT: D 31 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7592 (mm-30) REVERT: D 33 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8685 (tptt) REVERT: D 53 HIS cc_start: 0.8580 (m90) cc_final: 0.7610 (m90) REVERT: D 109 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6754 (ttm170) REVERT: D 153 GLU cc_start: 0.8897 (mp0) cc_final: 0.8559 (mp0) REVERT: F 134 MET cc_start: 0.8710 (ttt) cc_final: 0.8339 (ttt) REVERT: F 135 ASP cc_start: 0.8623 (t0) cc_final: 0.8141 (t0) REVERT: F 138 CYS cc_start: 0.8275 (m) cc_final: 0.7882 (m) REVERT: F 322 LYS cc_start: 0.8591 (mtmt) cc_final: 0.7924 (mttm) REVERT: G 201 LEU cc_start: 0.5197 (OUTLIER) cc_final: 0.4780 (mm) REVERT: G 316 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8057 (tm-30) REVERT: I 298 PHE cc_start: 0.6917 (p90) cc_final: 0.6418 (p90) REVERT: I 322 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8558 (mtpp) REVERT: J 304 LYS cc_start: 0.8944 (pptt) cc_final: 0.8709 (pptt) REVERT: J 322 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8483 (mtmt) REVERT: K 23 MET cc_start: 0.8998 (tpp) cc_final: 0.8526 (tpt) REVERT: K 135 ASP cc_start: 0.8695 (t0) cc_final: 0.8202 (t0) REVERT: K 311 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7941 (tp30) REVERT: L 23 MET cc_start: 0.7689 (tmm) cc_final: 0.7289 (tpt) REVERT: L 74 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7643 (tm-30) REVERT: L 78 TYR cc_start: 0.8433 (m-10) cc_final: 0.8064 (m-10) outliers start: 88 outliers final: 64 residues processed: 420 average time/residue: 0.3883 time to fit residues: 257.8776 Evaluate side-chains 406 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 338 time to evaluate : 2.848 ------------------------------------------------------------------------------- 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 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 31 GLU 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 109 ARG 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 220 LEU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU 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 348 LEU Chi-restraints excluded: chain F residue 171 LEU 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 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 74 GLU Chi-restraints excluded: chain H residue 117 THR 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 45 THR 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 292 LEU 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 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 72 SER Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 315 ILE Chi-restraints excluded: chain L residue 325 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 288 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 259 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.123266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.085889 restraints weight = 47824.385| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.49 r_work: 0.3054 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24764 Z= 0.206 Angle : 0.546 8.016 33586 Z= 0.277 Chirality : 0.040 0.174 3830 Planarity : 0.003 0.035 4246 Dihedral : 5.162 76.692 3407 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.12 % Allowed : 27.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.16), residues: 2944 helix: 2.22 (0.12), residues: 1974 sheet: 0.77 (0.32), residues: 330 loop : -1.15 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 16 HIS 0.004 0.001 HIS F 101 PHE 0.028 0.001 PHE G 298 TYR 0.019 0.001 TYR E 303 ARG 0.005 0.000 ARG K 314 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 1611) hydrogen bonds : angle 3.84929 ( 4716) SS BOND : bond 0.00310 ( 6) SS BOND : angle 1.71524 ( 12) covalent geometry : bond 0.00486 (24758) covalent geometry : angle 0.54496 (33574) *********************** 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 489 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 357 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6890 (mmt) cc_final: 0.6442 (mmm) REVERT: A 138 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9137 (tt) REVERT: B 183 ASN cc_start: 0.8397 (t0) cc_final: 0.8035 (t0) REVERT: C 14 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7586 (ttp80) REVERT: D 31 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7685 (mm-30) REVERT: D 33 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8729 (tptt) REVERT: D 53 HIS cc_start: 0.8584 (m90) cc_final: 0.7869 (m-70) REVERT: D 109 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6812 (ttm170) REVERT: D 153 GLU cc_start: 0.8947 (mp0) cc_final: 0.8584 (mp0) REVERT: E 340 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8292 (mtp180) REVERT: F 134 MET cc_start: 0.8820 (ttt) cc_final: 0.8444 (ttt) REVERT: F 135 ASP cc_start: 0.8590 (t0) cc_final: 0.8117 (t0) REVERT: F 138 CYS cc_start: 0.8330 (m) cc_final: 0.8073 (m) REVERT: F 322 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8036 (mttm) REVERT: G 201 LEU cc_start: 0.5117 (OUTLIER) cc_final: 0.4692 (mm) REVERT: G 316 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8107 (tm-30) REVERT: J 301 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7627 (p0) REVERT: J 304 LYS cc_start: 0.8949 (pptt) cc_final: 0.8732 (pptt) REVERT: J 322 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8410 (mtmt) REVERT: J 324 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8828 (tt) REVERT: J 340 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.5982 (mmm160) REVERT: K 135 ASP cc_start: 0.8718 (t0) cc_final: 0.8233 (t0) REVERT: K 311 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7971 (tp30) REVERT: K 368 ASP cc_start: 0.8580 (t70) cc_final: 0.8280 (t0) REVERT: L 23 MET cc_start: 0.7788 (tmm) cc_final: 0.7223 (tpt) outliers start: 132 outliers final: 98 residues processed: 455 average time/residue: 0.3465 time to fit residues: 247.3668 Evaluate side-chains 452 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 345 time to evaluate : 2.694 ------------------------------------------------------------------------------- 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 102 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 170 SER 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 31 GLU 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 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 251 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 136 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 200 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 72 SER 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 21 LEU 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 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 184 GLU 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 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 34 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 162 GLU 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 324 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 340 ARG Chi-restraints excluded: chain J residue 358 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 131 GLU 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 311 GLU Chi-restraints excluded: chain K residue 325 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 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 360 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 104 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 292 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.124339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.086094 restraints weight = 47983.961| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.53 r_work: 0.3074 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- 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: 0.8531 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24764 Z= 0.150 Angle : 0.523 9.007 33586 Z= 0.265 Chirality : 0.039 0.197 3830 Planarity : 0.003 0.041 4246 Dihedral : 4.997 83.009 3407 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.36 % Allowed : 27.41 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.16), residues: 2944 helix: 2.28 (0.12), residues: 1974 sheet: 0.78 (0.32), residues: 330 loop : -1.12 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 16 HIS 0.005 0.001 HIS F 101 PHE 0.028 0.001 PHE G 298 TYR 0.018 0.001 TYR B 126 ARG 0.006 0.000 ARG K 314 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 1611) hydrogen bonds : angle 3.77345 ( 4716) SS BOND : bond 0.00349 ( 6) SS BOND : angle 1.48855 ( 12) covalent geometry : bond 0.00349 (24758) covalent geometry : angle 0.52188 (33574) *********************** 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 489 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 351 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6925 (mmt) cc_final: 0.6389 (mmm) REVERT: A 138 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9031 (tp) REVERT: B 183 ASN cc_start: 0.8483 (t0) cc_final: 0.8104 (t0) REVERT: C 14 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7636 (ttp80) REVERT: C 96 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8358 (ttm) REVERT: D 31 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7718 (mm-30) REVERT: D 33 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8713 (tptt) REVERT: D 53 HIS cc_start: 0.8622 (m90) cc_final: 0.7621 (m90) REVERT: D 109 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6912 (ttm170) REVERT: D 153 GLU cc_start: 0.9052 (mp0) cc_final: 0.8696 (mp0) REVERT: F 135 ASP cc_start: 0.8728 (t0) cc_final: 0.8200 (t0) REVERT: F 138 CYS cc_start: 0.8723 (m) cc_final: 0.8492 (m) REVERT: F 322 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8029 (mttm) REVERT: G 201 LEU cc_start: 0.5134 (OUTLIER) cc_final: 0.4688 (mm) REVERT: H 193 ARG cc_start: 0.6905 (ptp90) cc_final: 0.6657 (ptt-90) REVERT: I 298 PHE cc_start: 0.6576 (p90) cc_final: 0.5833 (p90) REVERT: I 322 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8552 (mtpp) REVERT: J 134 MET cc_start: 0.9358 (ttt) cc_final: 0.9059 (ttt) REVERT: J 301 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7625 (p0) REVERT: J 304 LYS cc_start: 0.9008 (pptt) cc_final: 0.8807 (pptt) REVERT: J 322 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8560 (mtmt) REVERT: K 23 MET cc_start: 0.9057 (tpp) cc_final: 0.8604 (tpt) REVERT: K 135 ASP cc_start: 0.8784 (t0) cc_final: 0.8259 (t0) REVERT: K 311 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8004 (tp30) REVERT: K 368 ASP cc_start: 0.8659 (t70) cc_final: 0.8370 (t0) REVERT: L 23 MET cc_start: 0.7788 (tmm) cc_final: 0.7179 (tpt) REVERT: L 74 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8148 (tm-30) REVERT: L 322 LYS cc_start: 0.9173 (mtpp) cc_final: 0.8851 (mtpp) outliers start: 138 outliers final: 107 residues processed: 459 average time/residue: 0.3947 time to fit residues: 288.4470 Evaluate side-chains 459 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 345 time to evaluate : 2.762 ------------------------------------------------------------------------------- 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 102 MET Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 170 SER 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 62 VAL 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 149 ILE Chi-restraints excluded: chain B residue 167 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 96 MET 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 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 251 LEU Chi-restraints excluded: chain C residue 259 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 136 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 200 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 258 MET 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 168 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 21 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 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 45 THR 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 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 162 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain J residue 323 SER Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 351 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 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 Chi-restraints excluded: chain L residue 360 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 259 optimal weight: 5.9990 chunk 282 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 229 optimal weight: 0.3980 chunk 197 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.124560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087513 restraints weight = 47474.290| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.46 r_work: 0.3095 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24764 Z= 0.123 Angle : 0.510 8.615 33586 Z= 0.256 Chirality : 0.039 0.189 3830 Planarity : 0.003 0.034 4246 Dihedral : 4.838 89.919 3407 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.05 % Allowed : 28.03 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.16), residues: 2944 helix: 2.36 (0.12), residues: 1970 sheet: 0.83 (0.32), residues: 328 loop : -1.05 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 16 HIS 0.005 0.001 HIS F 101 PHE 0.028 0.001 PHE G 298 TYR 0.021 0.001 TYR E 303 ARG 0.006 0.000 ARG K 314 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 1611) hydrogen bonds : angle 3.69353 ( 4716) SS BOND : bond 0.00297 ( 6) SS BOND : angle 1.49485 ( 12) covalent geometry : bond 0.00278 (24758) covalent geometry : angle 0.50955 (33574) *********************** 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 481 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 351 time to evaluate : 5.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6716 (mmt) cc_final: 0.6260 (mmm) REVERT: C 14 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7477 (ttp80) REVERT: D 33 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8707 (tptt) REVERT: D 53 HIS cc_start: 0.8573 (m90) cc_final: 0.7610 (m90) REVERT: D 109 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6757 (ttm170) REVERT: D 153 GLU cc_start: 0.8911 (mp0) cc_final: 0.8565 (mp0) REVERT: F 135 ASP cc_start: 0.8639 (t0) cc_final: 0.8180 (t0) REVERT: F 138 CYS cc_start: 0.8345 (m) cc_final: 0.8113 (m) REVERT: F 322 LYS cc_start: 0.8624 (mtmt) cc_final: 0.7985 (mttm) REVERT: G 201 LEU cc_start: 0.5190 (OUTLIER) cc_final: 0.4774 (mm) REVERT: G 316 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8235 (tm-30) REVERT: I 298 PHE cc_start: 0.6530 (p90) cc_final: 0.5583 (p90) REVERT: I 322 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8525 (mtpp) REVERT: J 134 MET cc_start: 0.9163 (ttt) cc_final: 0.8852 (ttt) REVERT: J 301 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7606 (p0) REVERT: J 304 LYS cc_start: 0.9011 (pptt) cc_final: 0.8790 (pptt) REVERT: J 322 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8499 (mtmt) REVERT: J 340 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6059 (mmm160) REVERT: K 23 MET cc_start: 0.8940 (tpp) cc_final: 0.8376 (tpt) REVERT: K 135 ASP cc_start: 0.8715 (t0) cc_final: 0.8237 (t0) REVERT: K 311 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: K 368 ASP cc_start: 0.8742 (t70) cc_final: 0.8430 (t0) REVERT: L 23 MET cc_start: 0.7753 (tmm) cc_final: 0.7159 (tpt) REVERT: L 74 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7940 (tm-30) outliers start: 130 outliers final: 107 residues processed: 454 average time/residue: 0.5180 time to fit residues: 379.2179 Evaluate side-chains 454 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 341 time to evaluate : 5.185 ------------------------------------------------------------------------------- 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 170 SER 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 62 VAL 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 122 MET Chi-restraints excluded: chain C residue 123 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 136 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 200 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 258 MET 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 168 VAL 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 331 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 21 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 365 THR Chi-restraints excluded: chain G residue 34 SER 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 74 GLU Chi-restraints excluded: chain H residue 117 THR 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 45 THR 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 349 LEU 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 301 ASP Chi-restraints excluded: chain J residue 323 SER Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 340 ARG 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 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 Chi-restraints excluded: chain L residue 360 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 128 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 243 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.124872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087997 restraints weight = 47647.499| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.42 r_work: 0.3093 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 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 = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24764 Z= 0.141 Angle : 0.528 8.317 33586 Z= 0.265 Chirality : 0.039 0.213 3830 Planarity : 0.003 0.034 4246 Dihedral : 4.825 89.216 3407 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.85 % Allowed : 28.22 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.16), residues: 2944 helix: 2.34 (0.12), residues: 1972 sheet: 0.80 (0.32), residues: 328 loop : -1.05 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 16 HIS 0.004 0.001 HIS F 101 PHE 0.028 0.001 PHE G 298 TYR 0.016 0.001 TYR B 126 ARG 0.011 0.000 ARG H 193 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 1611) hydrogen bonds : angle 3.70123 ( 4716) SS BOND : bond 0.00278 ( 6) SS BOND : angle 1.82982 ( 12) covalent geometry : bond 0.00328 (24758) covalent geometry : angle 0.52664 (33574) *********************** 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 468 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 343 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7029 (mmt) cc_final: 0.6458 (mmm) REVERT: A 138 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9048 (tp) REVERT: C 14 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7505 (ttp80) REVERT: D 33 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8713 (tptt) REVERT: D 53 HIS cc_start: 0.8587 (m90) cc_final: 0.7613 (m90) REVERT: D 109 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6906 (ttm170) REVERT: D 153 GLU cc_start: 0.9022 (mp0) cc_final: 0.8675 (mp0) REVERT: F 23 MET cc_start: 0.8675 (mmm) cc_final: 0.8449 (tpt) REVERT: F 135 ASP cc_start: 0.8717 (t0) cc_final: 0.8186 (t0) REVERT: F 138 CYS cc_start: 0.8642 (m) cc_final: 0.8425 (m) REVERT: F 322 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8002 (mttm) REVERT: G 201 LEU cc_start: 0.5123 (OUTLIER) cc_final: 0.4672 (mm) REVERT: G 316 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8262 (tm-30) REVERT: H 193 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6975 (ptp90) REVERT: I 322 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8546 (mtpp) REVERT: J 301 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7685 (p0) REVERT: J 322 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8496 (mtmt) REVERT: J 324 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8769 (tt) REVERT: J 340 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6258 (mmm160) REVERT: K 23 MET cc_start: 0.8999 (tpp) cc_final: 0.8517 (tpt) REVERT: K 135 ASP cc_start: 0.8783 (t0) cc_final: 0.8242 (t0) REVERT: K 311 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: K 368 ASP cc_start: 0.8788 (t70) cc_final: 0.8474 (t0) REVERT: L 23 MET cc_start: 0.7769 (tmm) cc_final: 0.7138 (tpt) REVERT: L 86 MET cc_start: 0.9120 (tpt) cc_final: 0.8906 (tpt) outliers start: 125 outliers final: 112 residues processed: 440 average time/residue: 0.3566 time to fit residues: 245.4709 Evaluate side-chains 462 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 341 time to evaluate : 2.991 ------------------------------------------------------------------------------- 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 138 LEU Chi-restraints excluded: chain A residue 170 SER 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 62 VAL 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 122 MET Chi-restraints excluded: chain C residue 123 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 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 220 LEU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 168 VAL 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 331 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 21 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 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 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 193 ARG 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 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 349 LEU 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 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 340 ARG 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 296 VAL Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL 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 Chi-restraints excluded: chain L residue 360 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 178 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 198 optimal weight: 0.0770 chunk 51 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 220 optimal weight: 0.5980 chunk 259 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 overall best weight: 2.1344 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.123735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085335 restraints weight = 48412.708| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.55 r_work: 0.3059 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24764 Z= 0.195 Angle : 0.562 8.211 33586 Z= 0.284 Chirality : 0.041 0.202 3830 Planarity : 0.003 0.035 4246 Dihedral : 4.922 85.433 3407 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.28 % Allowed : 27.99 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.16), residues: 2944 helix: 2.26 (0.12), residues: 1971 sheet: 0.75 (0.32), residues: 328 loop : -1.12 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 45 HIS 0.004 0.001 HIS F 101 PHE 0.028 0.001 PHE G 298 TYR 0.023 0.001 TYR E 303 ARG 0.010 0.000 ARG H 193 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 1611) hydrogen bonds : angle 3.79295 ( 4716) SS BOND : bond 0.00301 ( 6) SS BOND : angle 2.07210 ( 12) covalent geometry : bond 0.00462 (24758) covalent geometry : angle 0.56080 (33574) *********************** 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 482 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 346 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6904 (mmt) cc_final: 0.6434 (mmm) REVERT: A 69 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8431 (p) REVERT: A 138 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9002 (tp) REVERT: B 183 ASN cc_start: 0.8341 (t0) cc_final: 0.7864 (t0) REVERT: C 14 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7511 (ttp80) REVERT: D 33 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8713 (tptt) REVERT: D 53 HIS cc_start: 0.8563 (m90) cc_final: 0.7562 (m90) REVERT: D 109 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6790 (ttm170) REVERT: D 153 GLU cc_start: 0.8961 (mp0) cc_final: 0.8543 (mp0) REVERT: F 14 LEU cc_start: 0.8806 (tp) cc_final: 0.8592 (tt) REVERT: F 23 MET cc_start: 0.8563 (mmm) cc_final: 0.8347 (tpt) REVERT: F 135 ASP cc_start: 0.8616 (t0) cc_final: 0.8118 (t0) REVERT: F 322 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8054 (mttm) REVERT: G 201 LEU cc_start: 0.5169 (OUTLIER) cc_final: 0.4695 (mm) REVERT: G 316 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8185 (tm-30) REVERT: H 193 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6928 (ptp90) REVERT: I 322 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8571 (mtpp) REVERT: J 322 LYS cc_start: 0.8850 (mtmt) cc_final: 0.8482 (mtmt) REVERT: J 324 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8799 (tt) REVERT: J 340 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.5940 (mmm160) REVERT: K 23 MET cc_start: 0.8987 (tpp) cc_final: 0.8484 (tpt) REVERT: K 135 ASP cc_start: 0.8747 (t0) cc_final: 0.8234 (t0) REVERT: K 311 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: K 368 ASP cc_start: 0.8630 (t70) cc_final: 0.8346 (t0) REVERT: L 74 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8114 (tm-30) outliers start: 136 outliers final: 117 residues processed: 454 average time/residue: 0.3544 time to fit residues: 251.4471 Evaluate side-chains 467 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 341 time to evaluate : 2.685 ------------------------------------------------------------------------------- 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 69 SER 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 138 LEU Chi-restraints excluded: chain A residue 170 SER 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 62 VAL 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 B residue 167 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 122 MET Chi-restraints excluded: chain C residue 123 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 251 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 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 220 LEU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 168 VAL 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 331 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 6 VAL 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 34 SER Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 182 PHE Chi-restraints excluded: chain G residue 187 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 74 GLU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 193 ARG 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 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 349 LEU Chi-restraints excluded: chain I residue 354 LEU 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 117 THR 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 331 VAL Chi-restraints excluded: chain J residue 340 ARG 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 296 VAL Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL 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 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 196 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 chunk 279 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 176 optimal weight: 0.0010 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 185 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- 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 = 0.124974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.086951 restraints weight = 48045.652| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.53 r_work: 0.3086 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 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 = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24764 Z= 0.136 Angle : 0.545 10.785 33586 Z= 0.273 Chirality : 0.040 0.215 3830 Planarity : 0.003 0.034 4246 Dihedral : 4.847 89.716 3407 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.85 % Allowed : 28.42 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.16), residues: 2944 helix: 2.29 (0.12), residues: 1969 sheet: 0.85 (0.32), residues: 326 loop : -1.13 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 16 HIS 0.005 0.001 HIS F 101 PHE 0.028 0.001 PHE G 298 TYR 0.023 0.001 TYR A 19 ARG 0.010 0.000 ARG H 193 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 1611) hydrogen bonds : angle 3.73014 ( 4716) SS BOND : bond 0.00253 ( 6) SS BOND : angle 1.59342 ( 12) covalent geometry : bond 0.00311 (24758) covalent geometry : angle 0.54470 (33574) ********************** 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 468 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 343 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7173 (mmt) cc_final: 0.6615 (mmm) REVERT: A 69 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8549 (p) REVERT: A 89 LYS cc_start: 0.8520 (mttt) cc_final: 0.8231 (mmtp) REVERT: A 138 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9047 (tp) REVERT: A 140 MET cc_start: 0.8590 (mmm) cc_final: 0.8025 (tpp) REVERT: B 183 ASN cc_start: 0.8442 (t0) cc_final: 0.7997 (t0) REVERT: C 14 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7578 (ttp80) REVERT: D 33 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8739 (tptt) REVERT: D 53 HIS cc_start: 0.8595 (m90) cc_final: 0.7588 (m90) REVERT: D 109 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6904 (ttm170) REVERT: D 153 GLU cc_start: 0.9019 (mp0) cc_final: 0.8665 (mp0) REVERT: F 135 ASP cc_start: 0.8834 (t0) cc_final: 0.8026 (t0) REVERT: F 138 CYS cc_start: 0.8223 (m) cc_final: 0.7465 (m) REVERT: F 322 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8071 (mttm) REVERT: G 201 LEU cc_start: 0.5128 (OUTLIER) cc_final: 0.4658 (mm) REVERT: G 316 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8216 (tm-30) REVERT: H 193 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6994 (ptp90) REVERT: I 189 ARG cc_start: 0.8211 (ttt180) cc_final: 0.7997 (ttt180) REVERT: I 322 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8574 (mtpp) REVERT: J 75 ASP cc_start: 0.8428 (m-30) cc_final: 0.8095 (t0) REVERT: J 322 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8376 (mtmt) REVERT: J 324 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8710 (tt) REVERT: J 340 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6322 (mmm160) REVERT: K 23 MET cc_start: 0.9024 (tpp) cc_final: 0.8470 (tpt) REVERT: K 135 ASP cc_start: 0.8818 (t0) cc_final: 0.8289 (t0) REVERT: K 181 GLN cc_start: 0.8776 (tt0) cc_final: 0.8353 (tp-100) REVERT: K 311 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: K 368 ASP cc_start: 0.8703 (t70) cc_final: 0.8417 (t0) REVERT: L 23 MET cc_start: 0.8093 (tmm) cc_final: 0.7307 (tpt) REVERT: L 74 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8270 (tm-30) outliers start: 125 outliers final: 114 residues processed: 442 average time/residue: 0.3575 time to fit residues: 246.7097 Evaluate side-chains 463 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 340 time to evaluate : 3.033 ------------------------------------------------------------------------------- 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 69 SER 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 138 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 170 SER 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 62 VAL 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 B residue 167 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 122 MET Chi-restraints excluded: chain C residue 123 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 251 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 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 220 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 168 VAL 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 331 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 6 VAL 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 34 SER Chi-restraints excluded: chain G residue 136 ASP 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 193 ARG 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 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 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 117 THR 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 340 ARG 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 296 VAL 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 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 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 62 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 266 optimal weight: 0.5980 chunk 26 optimal weight: 0.0070 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.3204 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.123446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.086332 restraints weight = 47568.959| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.42 r_work: 0.3065 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 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 = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24764 Z= 0.207 Angle : 0.580 10.497 33586 Z= 0.292 Chirality : 0.042 0.221 3830 Planarity : 0.003 0.035 4246 Dihedral : 4.954 85.558 3407 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.20 % Allowed : 28.14 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.16), residues: 2944 helix: 2.21 (0.12), residues: 1972 sheet: 0.80 (0.32), residues: 326 loop : -1.18 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 16 HIS 0.004 0.001 HIS F 101 PHE 0.028 0.001 PHE G 298 TYR 0.012 0.001 TYR G 303 ARG 0.010 0.000 ARG H 193 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 1611) hydrogen bonds : angle 3.81380 ( 4716) SS BOND : bond 0.00299 ( 6) SS BOND : angle 1.98674 ( 12) covalent geometry : bond 0.00491 (24758) covalent geometry : angle 0.57861 (33574) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16633.57 seconds wall clock time: 287 minutes 37.84 seconds (17257.84 seconds total)