Starting phenix.real_space_refine on Wed Jul 24 00:00:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsh_41592/07_2024/8tsh_41592_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsh_41592/07_2024/8tsh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsh_41592/07_2024/8tsh_41592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsh_41592/07_2024/8tsh_41592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsh_41592/07_2024/8tsh_41592_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsh_41592/07_2024/8tsh_41592_neut.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 Residue "C GLU 178": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F GLU 311": "OE1" <-> "OE2" Residue "G GLU 316": "OE1" <-> "OE2" Residue "I GLU 184": "OE1" <-> "OE2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "J GLU 124": "OE1" <-> "OE2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K GLU 188": "OE1" <-> "OE2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "L GLU 328": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 13.11, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 9.63 Conformation dependent library (CDL) restraints added in 4.3 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: 2.25 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: 7.24 Time building geometry restraints manager: 10.44 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: 98.72 - 106.95: 629 106.95 - 115.18: 14788 115.18 - 123.42: 17404 123.42 - 131.65: 703 131.65 - 139.88: 50 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 2.440 nonbonded pdb=" OG SER C 167 " pdb=" OG SER C 252 " model vdw 2.247 2.440 nonbonded pdb=" O HIS J 101 " pdb=" OG1 THR J 104 " model vdw 2.248 2.440 nonbonded pdb=" O PHE L 111 " pdb=" OH TYR L 125 " model vdw 2.251 2.440 ... (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 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 61.120 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.500 ------------------------------------------------------------------------------- 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 0.051 24758 Z= 0.182 Angle : 0.565 10.101 33574 Z= 0.294 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 350 time to evaluate : 2.764 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: 0.3582 time to fit residues: 195.1533 Evaluate side-chains 334 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 331 time to evaluate : 2.732 ------------------------------------------------------------------------------- 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: 0.9980 chunk 223 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 24758 Z= 0.459 Angle : 0.598 7.905 33574 Z= 0.308 Chirality : 0.042 0.180 3830 Planarity : 0.004 0.045 4246 Dihedral : 5.725 75.954 3413 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.43 % Allowed : 27.37 % Favored : 67.20 % 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: 1.84 (0.16), residues: 2944 helix: 2.02 (0.12), residues: 1965 sheet: 0.82 (0.32), residues: 332 loop : -1.11 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 342 HIS 0.005 0.001 HIS G 101 PHE 0.027 0.002 PHE G 298 TYR 0.018 0.002 TYR E 303 ARG 0.006 0.000 ARG F 129 *********************** 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 481 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 341 time to evaluate : 2.775 Fit side-chains REVERT: D 33 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8659 (tptt) REVERT: D 49 GLU cc_start: 0.8454 (tp30) cc_final: 0.8091 (tp30) REVERT: D 53 HIS cc_start: 0.8468 (m90) cc_final: 0.7573 (m90) REVERT: F 23 MET cc_start: 0.8656 (tpt) cc_final: 0.8424 (mmm) REVERT: F 135 ASP cc_start: 0.8437 (t0) cc_final: 0.7985 (t0) REVERT: F 138 CYS cc_start: 0.8155 (m) cc_final: 0.7817 (m) REVERT: F 314 ARG cc_start: 0.8403 (tmm160) cc_final: 0.8202 (tmm160) REVERT: G 303 TYR cc_start: 0.7155 (t80) cc_final: 0.6593 (t80) REVERT: G 316 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8076 (tm-30) REVERT: J 36 ASP cc_start: 0.9234 (OUTLIER) cc_final: 0.8909 (p0) REVERT: J 135 ASP cc_start: 0.8669 (t0) cc_final: 0.8275 (t0) REVERT: J 304 LYS cc_start: 0.8900 (pptt) cc_final: 0.8683 (pptt) REVERT: J 314 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7381 (tmm160) REVERT: J 324 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8960 (tt) REVERT: J 340 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6114 (mmm160) REVERT: K 135 ASP cc_start: 0.8579 (t0) cc_final: 0.7987 (t0) REVERT: K 368 ASP cc_start: 0.8585 (t70) cc_final: 0.8293 (t0) REVERT: L 23 MET cc_start: 0.7706 (tmm) cc_final: 0.7159 (tpt) REVERT: L 74 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8010 (tm-30) REVERT: L 324 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9074 (tt) outliers start: 140 outliers final: 92 residues processed: 450 average time/residue: 0.3446 time to fit residues: 242.7647 Evaluate side-chains 421 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 324 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 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 212 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 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 171 LEU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 291 ASP 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 187 LEU Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 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 36 ASP Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 314 ARG 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 325 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 142 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 268 optimal weight: 0.9980 chunk 289 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24758 Z= 0.211 Angle : 0.495 8.136 33574 Z= 0.252 Chirality : 0.039 0.164 3830 Planarity : 0.003 0.038 4246 Dihedral : 5.421 67.001 3409 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.96 % Allowed : 28.65 % Favored : 67.39 % 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: 2.25 (0.12), residues: 1969 sheet: 0.83 (0.32), residues: 332 loop : -1.00 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 342 HIS 0.005 0.001 HIS F 101 PHE 0.027 0.001 PHE G 298 TYR 0.013 0.001 TYR G 303 ARG 0.005 0.000 ARG K 314 *********************** 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 450 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 348 time to evaluate : 2.716 Fit side-chains revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8337 (t0) cc_final: 0.8040 (t0) REVERT: C 14 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7753 (ttp80) REVERT: D 33 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8547 (tptt) REVERT: D 53 HIS cc_start: 0.8644 (m90) cc_final: 0.7675 (m90) REVERT: F 134 MET cc_start: 0.8200 (ttt) cc_final: 0.7857 (ttt) REVERT: F 135 ASP cc_start: 0.8377 (t0) cc_final: 0.7918 (t0) REVERT: F 138 CYS cc_start: 0.8196 (m) cc_final: 0.7846 (m) REVERT: F 179 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: G 303 TYR cc_start: 0.7146 (t80) cc_final: 0.6574 (t80) REVERT: G 316 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8130 (tm-30) REVERT: J 36 ASP cc_start: 0.9213 (OUTLIER) cc_final: 0.8955 (p0) REVERT: J 135 ASP cc_start: 0.8730 (t0) cc_final: 0.8491 (t0) REVERT: J 304 LYS cc_start: 0.8980 (pptt) cc_final: 0.8745 (pptt) REVERT: J 314 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7314 (tmm160) REVERT: J 322 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8094 (mtmt) REVERT: K 135 ASP cc_start: 0.8550 (t0) cc_final: 0.7981 (t0) REVERT: K 311 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7647 (tp30) REVERT: K 368 ASP cc_start: 0.8640 (t70) cc_final: 0.8346 (t0) REVERT: L 23 MET cc_start: 0.7634 (tmm) cc_final: 0.7264 (tpt) REVERT: L 74 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7378 (tm-30) REVERT: L 78 TYR cc_start: 0.8128 (m-10) cc_final: 0.7608 (m-10) outliers start: 102 outliers final: 66 residues processed: 426 average time/residue: 0.3563 time to fit residues: 235.5807 Evaluate side-chains 406 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 335 time to evaluate : 2.775 ------------------------------------------------------------------------------- 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 157 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 149 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 199 VAL 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 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 200 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 179 GLN Chi-restraints excluded: chain F residue 291 ASP 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 136 ASP 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 168 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 45 THR 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 36 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 182 PHE Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 296 VAL Chi-restraints excluded: chain L residue 325 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 285 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 255 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 179 GLN I 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24758 Z= 0.204 Angle : 0.494 11.956 33574 Z= 0.250 Chirality : 0.038 0.191 3830 Planarity : 0.003 0.036 4246 Dihedral : 5.269 65.599 3407 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.58 % Allowed : 28.61 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.33 (0.12), residues: 1970 sheet: 0.82 (0.32), residues: 334 loop : -0.95 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 16 HIS 0.004 0.001 HIS F 101 PHE 0.027 0.001 PHE G 298 TYR 0.019 0.001 TYR E 303 ARG 0.005 0.000 ARG K 314 *********************** 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 469 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 351 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8327 (t0) cc_final: 0.7976 (t0) REVERT: C 14 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7685 (ttp80) REVERT: D 33 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8540 (tptt) REVERT: D 49 GLU cc_start: 0.8722 (tp30) cc_final: 0.8174 (tp30) REVERT: D 53 HIS cc_start: 0.8631 (m90) cc_final: 0.7616 (m90) REVERT: D 109 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6902 (ttm170) REVERT: F 23 MET cc_start: 0.8720 (mmm) cc_final: 0.8467 (tpt) REVERT: F 134 MET cc_start: 0.8245 (ttt) cc_final: 0.7906 (ttt) REVERT: F 135 ASP cc_start: 0.8384 (t0) cc_final: 0.7925 (t0) REVERT: F 138 CYS cc_start: 0.8222 (m) cc_final: 0.7939 (m) REVERT: G 316 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8142 (tm-30) REVERT: J 36 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8939 (p0) REVERT: J 135 ASP cc_start: 0.8738 (t0) cc_final: 0.8451 (t0) REVERT: J 304 LYS cc_start: 0.8978 (pptt) cc_final: 0.8754 (pptt) REVERT: J 324 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8790 (tt) REVERT: K 23 MET cc_start: 0.9009 (tpp) cc_final: 0.8554 (tpt) REVERT: K 135 ASP cc_start: 0.8533 (t0) cc_final: 0.7966 (t0) REVERT: K 181 GLN cc_start: 0.8757 (tt0) cc_final: 0.8368 (tp-100) REVERT: K 311 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7601 (tp30) REVERT: K 368 ASP cc_start: 0.8649 (t70) cc_final: 0.8359 (t0) REVERT: L 23 MET cc_start: 0.7665 (tmm) cc_final: 0.7271 (tpt) outliers start: 118 outliers final: 94 residues processed: 444 average time/residue: 0.3344 time to fit residues: 232.6570 Evaluate side-chains 434 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 335 time to evaluate : 2.733 ------------------------------------------------------------------------------- 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 157 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 149 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 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 289 PHE Chi-restraints excluded: chain F residue 291 ASP 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 136 ASP Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 42 SER 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 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 34 SER Chi-restraints excluded: chain J residue 36 ASP 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 164 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 292 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 358 VAL Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 182 PHE Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain L residue 45 THR 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 325 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 chunk 197 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 255 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 200 GLN I 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 24758 Z= 0.460 Angle : 0.602 8.057 33574 Z= 0.307 Chirality : 0.043 0.185 3830 Planarity : 0.004 0.038 4246 Dihedral : 5.371 71.051 3407 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 6.72 % Allowed : 27.41 % Favored : 65.88 % 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: 1.88 (0.16), residues: 2944 helix: 2.09 (0.12), residues: 1970 sheet: 0.74 (0.32), residues: 334 loop : -1.19 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 16 HIS 0.005 0.001 HIS G 101 PHE 0.028 0.002 PHE G 298 TYR 0.014 0.002 TYR E 82 ARG 0.006 0.000 ARG K 314 *********************** 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 524 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 351 time to evaluate : 3.025 Fit side-chains revert: symmetry clash REVERT: A 69 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8558 (p) REVERT: B 86 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8339 (pt0) REVERT: B 183 ASN cc_start: 0.8517 (t0) cc_final: 0.8097 (t0) REVERT: B 185 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.7137 (m-40) REVERT: C 14 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7775 (ttp80) REVERT: D 33 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8589 (tptt) REVERT: D 53 HIS cc_start: 0.8599 (m90) cc_final: 0.7745 (m90) REVERT: E 340 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8172 (mtp180) REVERT: F 23 MET cc_start: 0.8759 (mmm) cc_final: 0.8477 (tpt) REVERT: F 134 MET cc_start: 0.8522 (ttt) cc_final: 0.8187 (ttt) REVERT: F 135 ASP cc_start: 0.8407 (t0) cc_final: 0.7978 (t0) REVERT: G 316 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8205 (tm-30) REVERT: J 135 ASP cc_start: 0.8829 (t0) cc_final: 0.8571 (t0) REVERT: J 304 LYS cc_start: 0.8994 (pptt) cc_final: 0.8774 (pptt) REVERT: J 324 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8948 (tt) REVERT: J 340 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6085 (mmm160) REVERT: K 23 MET cc_start: 0.9089 (tpp) cc_final: 0.8614 (tpt) REVERT: K 135 ASP cc_start: 0.8516 (t0) cc_final: 0.7920 (t0) REVERT: K 311 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7679 (tp30) REVERT: K 368 ASP cc_start: 0.8671 (t70) cc_final: 0.8348 (t0) REVERT: L 23 MET cc_start: 0.7800 (tmm) cc_final: 0.7188 (tpt) REVERT: L 324 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9074 (tt) outliers start: 173 outliers final: 129 residues processed: 488 average time/residue: 0.3309 time to fit residues: 255.0835 Evaluate side-chains 478 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 340 time to evaluate : 2.709 ------------------------------------------------------------------------------- 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 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 127 SER 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 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 82 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 185 ASN 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 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 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 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 200 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 229 SER 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 117 THR Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 SER 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 325 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 106 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 291 ASP Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 187 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 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 168 VAL 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 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 305 LEU 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 97 LYS 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 164 SER Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 292 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 331 VAL Chi-restraints excluded: chain J residue 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 168 VAL Chi-restraints excluded: chain K residue 182 PHE Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 45 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 0.9980 chunk 256 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 285 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN H 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24758 Z= 0.181 Angle : 0.499 8.551 33574 Z= 0.252 Chirality : 0.038 0.181 3830 Planarity : 0.003 0.035 4246 Dihedral : 5.186 71.336 3407 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.27 % Allowed : 30.09 % Favored : 65.64 % 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: 2.34 (0.12), residues: 1974 sheet: 0.84 (0.32), residues: 334 loop : -0.99 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 16 HIS 0.004 0.001 HIS F 101 PHE 0.028 0.001 PHE G 298 TYR 0.022 0.001 TYR E 303 ARG 0.006 0.000 ARG K 314 *********************** 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 465 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 355 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8346 (pt0) REVERT: B 183 ASN cc_start: 0.8337 (t0) cc_final: 0.7954 (t0) REVERT: C 14 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7619 (ttp80) REVERT: D 33 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8617 (tptt) REVERT: D 53 HIS cc_start: 0.8630 (m90) cc_final: 0.7689 (m90) REVERT: D 109 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6799 (ttm170) REVERT: E 340 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8214 (mtp180) REVERT: F 135 ASP cc_start: 0.8390 (t0) cc_final: 0.7590 (t0) REVERT: F 138 CYS cc_start: 0.7610 (m) cc_final: 0.6867 (m) REVERT: F 179 GLN cc_start: 0.8083 (mp-120) cc_final: 0.7426 (mp10) REVERT: G 201 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4726 (mm) REVERT: G 316 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8298 (tm-30) REVERT: I 298 PHE cc_start: 0.6990 (p90) cc_final: 0.6478 (p90) REVERT: I 307 LEU cc_start: 0.9231 (mm) cc_final: 0.8886 (mm) REVERT: J 36 ASP cc_start: 0.9204 (OUTLIER) cc_final: 0.8946 (p0) REVERT: J 134 MET cc_start: 0.9226 (ttt) cc_final: 0.8962 (ttt) REVERT: J 135 ASP cc_start: 0.8831 (t0) cc_final: 0.8487 (t0) REVERT: J 301 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7551 (p0) REVERT: J 304 LYS cc_start: 0.9026 (pptt) cc_final: 0.8825 (pptt) REVERT: J 322 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8273 (mtmt) REVERT: K 23 MET cc_start: 0.8989 (tpp) cc_final: 0.8421 (tpt) REVERT: K 135 ASP cc_start: 0.8523 (t0) cc_final: 0.7960 (t0) REVERT: K 181 GLN cc_start: 0.8747 (tt0) cc_final: 0.8358 (tp-100) REVERT: K 311 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7621 (tp30) REVERT: K 368 ASP cc_start: 0.8654 (t70) cc_final: 0.8344 (t0) REVERT: L 23 MET cc_start: 0.7710 (tmm) cc_final: 0.7159 (tpt) outliers start: 110 outliers final: 87 residues processed: 445 average time/residue: 0.3406 time to fit residues: 235.9812 Evaluate side-chains 444 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 349 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 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 86 GLU Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain 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 163 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 229 SER 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 117 THR Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 36 ASP 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 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 117 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 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 36 ASP 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 136 ASP Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 164 SER 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 325 VAL Chi-restraints excluded: chain J residue 358 VAL 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 138 CYS Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 315 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 360 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 240 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24758 Z= 0.197 Angle : 0.503 8.395 33574 Z= 0.253 Chirality : 0.038 0.208 3830 Planarity : 0.003 0.035 4246 Dihedral : 5.074 74.748 3407 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.12 % Allowed : 29.54 % Favored : 65.33 % 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: 2.27 (0.16), residues: 2944 helix: 2.37 (0.12), residues: 1969 sheet: 0.87 (0.32), residues: 332 loop : -0.98 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 16 HIS 0.004 0.001 HIS F 101 PHE 0.028 0.001 PHE G 298 TYR 0.021 0.001 TYR D 194 ARG 0.007 0.000 ARG K 314 *********************** 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 487 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 355 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8323 (t0) cc_final: 0.7930 (t0) REVERT: C 14 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7536 (ttp80) REVERT: C 96 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8293 (ttm) REVERT: D 33 LYS cc_start: 0.8923 (mmmt) cc_final: 0.8615 (tptt) REVERT: D 53 HIS cc_start: 0.8624 (m90) cc_final: 0.7659 (m90) REVERT: D 109 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6899 (ttm170) REVERT: E 340 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8207 (mtp180) REVERT: F 135 ASP cc_start: 0.8392 (t0) cc_final: 0.7685 (t0) REVERT: F 138 CYS cc_start: 0.7583 (m) cc_final: 0.6765 (m) REVERT: F 179 GLN cc_start: 0.8100 (mp-120) cc_final: 0.7438 (mp10) REVERT: G 201 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.4760 (mm) REVERT: G 316 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8302 (tm-30) REVERT: H 314 ARG cc_start: 0.7996 (tmm160) cc_final: 0.7166 (tmm160) REVERT: I 298 PHE cc_start: 0.7009 (p90) cc_final: 0.6483 (p90) REVERT: I 307 LEU cc_start: 0.9242 (mm) cc_final: 0.8872 (mm) REVERT: J 36 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8928 (p0) REVERT: J 134 MET cc_start: 0.9208 (ttt) cc_final: 0.8926 (ttt) REVERT: J 135 ASP cc_start: 0.8810 (t0) cc_final: 0.8467 (t0) REVERT: J 301 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7566 (p0) REVERT: J 304 LYS cc_start: 0.9030 (pptt) cc_final: 0.8829 (pptt) REVERT: J 322 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8235 (mtmt) REVERT: K 23 MET cc_start: 0.8986 (tpp) cc_final: 0.8411 (tpt) REVERT: K 135 ASP cc_start: 0.8542 (t0) cc_final: 0.7967 (t0) REVERT: K 181 GLN cc_start: 0.8720 (tt0) cc_final: 0.8329 (tp-100) REVERT: K 311 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7578 (tp30) REVERT: K 368 ASP cc_start: 0.8658 (t70) cc_final: 0.8350 (t0) REVERT: L 23 MET cc_start: 0.7720 (tmm) cc_final: 0.7169 (tpt) outliers start: 132 outliers final: 109 residues processed: 460 average time/residue: 0.3527 time to fit residues: 255.1783 Evaluate side-chains 466 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 349 time to evaluate : 2.683 ------------------------------------------------------------------------------- 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 157 ASP 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 124 LYS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 149 ILE 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 127 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain 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 117 VAL 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 200 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 229 SER 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 117 THR Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 SER 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 340 ARG Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 36 ASP 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 291 ASP 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 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 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain 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 36 ASP 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 136 ASP Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 164 SER 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 358 VAL Chi-restraints excluded: chain K residue 104 THR 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 138 CYS Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 315 ILE Chi-restraints excluded: chain L residue 325 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 4.9990 chunk 113 optimal weight: 0.0970 chunk 169 optimal weight: 8.9990 chunk 85 optimal weight: 0.0470 chunk 55 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 26 optimal weight: 0.0020 chunk 223 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 overall best weight: 1.4288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24758 Z= 0.218 Angle : 0.519 8.409 33574 Z= 0.260 Chirality : 0.039 0.194 3830 Planarity : 0.003 0.062 4246 Dihedral : 4.996 77.484 3407 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.43 % Allowed : 29.31 % Favored : 65.26 % 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: 2.25 (0.16), residues: 2944 helix: 2.36 (0.12), residues: 1968 sheet: 0.87 (0.32), residues: 332 loop : -1.00 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 16 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 0.007 0.000 ARG K 314 *********************** 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 491 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 351 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8315 (t0) cc_final: 0.7920 (t0) REVERT: C 14 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7549 (ttp80) REVERT: C 96 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8278 (ttm) REVERT: D 33 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8621 (tptt) REVERT: D 53 HIS cc_start: 0.8604 (m90) cc_final: 0.7646 (m90) REVERT: D 109 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6883 (ttm170) REVERT: E 340 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8170 (mtp180) REVERT: F 135 ASP cc_start: 0.8393 (t0) cc_final: 0.7667 (t0) REVERT: F 138 CYS cc_start: 0.7581 (m) cc_final: 0.6765 (m) REVERT: G 97 LYS cc_start: 0.8960 (mtmm) cc_final: 0.8717 (mttp) REVERT: G 201 LEU cc_start: 0.5192 (OUTLIER) cc_final: 0.4772 (mm) REVERT: G 316 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8159 (tm-30) REVERT: I 23 MET cc_start: 0.8653 (mmm) cc_final: 0.8294 (mmm) REVERT: I 136 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: I 307 LEU cc_start: 0.9231 (mm) cc_final: 0.8859 (mm) REVERT: J 36 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8925 (p0) REVERT: J 134 MET cc_start: 0.9218 (ttt) cc_final: 0.8915 (ttt) REVERT: J 135 ASP cc_start: 0.8831 (t0) cc_final: 0.8478 (t0) REVERT: J 301 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7397 (p0) REVERT: J 304 LYS cc_start: 0.9032 (pptt) cc_final: 0.8768 (pptt) REVERT: J 305 LEU cc_start: 0.9281 (mt) cc_final: 0.8935 (mt) REVERT: J 314 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7364 (tmm160) REVERT: J 322 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8215 (mtmt) REVERT: J 340 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6065 (mmm160) REVERT: K 23 MET cc_start: 0.8988 (tpp) cc_final: 0.8407 (tpt) REVERT: K 135 ASP cc_start: 0.8541 (t0) cc_final: 0.7963 (t0) REVERT: K 181 GLN cc_start: 0.8719 (tt0) cc_final: 0.8339 (tp-100) REVERT: K 311 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: K 368 ASP cc_start: 0.8663 (t70) cc_final: 0.8352 (t0) REVERT: L 23 MET cc_start: 0.7772 (tmm) cc_final: 0.7181 (tpt) outliers start: 140 outliers final: 117 residues processed: 458 average time/residue: 0.3493 time to fit residues: 248.1445 Evaluate side-chains 474 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 346 time to evaluate : 2.647 ------------------------------------------------------------------------------- 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 62 VAL Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 157 ASP 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 124 LYS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 ILE 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 127 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 74 TYR 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 117 VAL 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 229 SER 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 117 THR Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 36 ASP 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 291 ASP 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 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 202 ILE Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 136 ASP 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 36 ASP 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 136 ASP Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain J residue 314 ARG 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 358 VAL Chi-restraints excluded: chain K residue 104 THR 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 331 VAL Chi-restraints excluded: chain K residue 366 ILE 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 300 GLU Chi-restraints excluded: chain L residue 315 ILE Chi-restraints excluded: chain L residue 325 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 5.9990 chunk 248 optimal weight: 0.5980 chunk 264 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 280 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24758 Z= 0.203 Angle : 0.522 8.333 33574 Z= 0.260 Chirality : 0.039 0.194 3830 Planarity : 0.003 0.038 4246 Dihedral : 4.901 82.072 3407 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.28 % Allowed : 29.58 % Favored : 65.14 % 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: 2.26 (0.16), residues: 2944 helix: 2.39 (0.12), residues: 1961 sheet: 0.88 (0.32), residues: 332 loop : -1.01 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 16 HIS 0.004 0.001 HIS F 101 PHE 0.029 0.001 PHE G 298 TYR 0.022 0.001 TYR D 194 ARG 0.007 0.000 ARG K 314 *********************** 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 487 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 351 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8307 (t0) cc_final: 0.7863 (t0) REVERT: B 185 ASN cc_start: 0.7348 (OUTLIER) cc_final: 0.7047 (m-40) REVERT: C 14 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7541 (ttp80) REVERT: C 96 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8285 (ttm) REVERT: D 33 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8620 (tptt) REVERT: D 53 HIS cc_start: 0.8491 (m90) cc_final: 0.7572 (m90) REVERT: D 109 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6872 (ttm170) REVERT: E 340 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8167 (mtp180) REVERT: F 135 ASP cc_start: 0.8422 (t0) cc_final: 0.7673 (t0) REVERT: F 138 CYS cc_start: 0.7468 (m) cc_final: 0.6635 (m) REVERT: G 201 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4673 (mm) REVERT: G 316 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8201 (tm-30) REVERT: I 136 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: I 298 PHE cc_start: 0.6607 (p90) cc_final: 0.6128 (p90) REVERT: I 307 LEU cc_start: 0.9255 (mm) cc_final: 0.8892 (mm) REVERT: J 36 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8910 (p0) REVERT: J 134 MET cc_start: 0.9207 (ttt) cc_final: 0.8930 (ttt) REVERT: J 135 ASP cc_start: 0.8819 (t0) cc_final: 0.8485 (t0) REVERT: J 301 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7516 (p0) REVERT: J 304 LYS cc_start: 0.9034 (pptt) cc_final: 0.8787 (pptt) REVERT: J 305 LEU cc_start: 0.9220 (mt) cc_final: 0.8855 (mt) REVERT: J 314 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7409 (tmm160) REVERT: J 322 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8194 (mtmt) REVERT: J 324 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8772 (tt) REVERT: J 340 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6051 (mmm160) REVERT: K 23 MET cc_start: 0.8978 (tpp) cc_final: 0.8389 (tpt) REVERT: K 135 ASP cc_start: 0.8540 (t0) cc_final: 0.7950 (t0) REVERT: K 181 GLN cc_start: 0.8711 (tt0) cc_final: 0.8295 (tp-100) REVERT: K 311 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: L 23 MET cc_start: 0.7743 (tmm) cc_final: 0.7156 (tpt) outliers start: 136 outliers final: 117 residues processed: 456 average time/residue: 0.3497 time to fit residues: 248.0269 Evaluate side-chains 475 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 345 time to evaluate : 2.709 ------------------------------------------------------------------------------- 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 157 ASP Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 204 LEU 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 124 LYS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 185 ASN 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 127 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 211 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 117 VAL 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 229 SER 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 117 THR Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 36 ASP 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 291 ASP 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 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 202 ILE Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 136 ASP 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 36 ASP 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 162 GLU Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain J residue 314 ARG 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 104 THR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 293 optimal weight: 6.9990 chunk 270 optimal weight: 0.6980 chunk 234 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 180 optimal weight: 0.5980 chunk 143 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 249 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24758 Z= 0.165 Angle : 0.508 8.190 33574 Z= 0.254 Chirality : 0.038 0.204 3830 Planarity : 0.003 0.041 4246 Dihedral : 4.752 87.773 3407 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.62 % Allowed : 30.05 % Favored : 65.33 % 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: 2.34 (0.16), residues: 2944 helix: 2.43 (0.12), residues: 1962 sheet: 0.99 (0.32), residues: 328 loop : -0.97 (0.24), residues: 654 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 0.029 0.001 PHE G 298 TYR 0.024 0.001 TYR E 303 ARG 0.007 0.000 ARG K 314 ********************** 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 474 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 355 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8359 (t0) cc_final: 0.7987 (t0) REVERT: C 14 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7535 (ttp80) REVERT: D 33 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8622 (tptt) REVERT: D 45 TRP cc_start: 0.8768 (t-100) cc_final: 0.8490 (t-100) REVERT: D 53 HIS cc_start: 0.8479 (m90) cc_final: 0.7545 (m90) REVERT: D 109 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6854 (ttm170) REVERT: E 340 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8174 (mtp180) REVERT: F 135 ASP cc_start: 0.8450 (t0) cc_final: 0.7818 (t0) REVERT: F 138 CYS cc_start: 0.7521 (m) cc_final: 0.6764 (m) REVERT: F 322 LYS cc_start: 0.8515 (mtmt) cc_final: 0.7998 (mttm) REVERT: G 201 LEU cc_start: 0.5185 (OUTLIER) cc_final: 0.4751 (mm) REVERT: G 316 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8235 (tm-30) REVERT: I 298 PHE cc_start: 0.6599 (p90) cc_final: 0.6124 (p90) REVERT: I 307 LEU cc_start: 0.9250 (mm) cc_final: 0.8884 (mm) REVERT: J 23 MET cc_start: 0.8088 (mmt) cc_final: 0.7836 (mmt) REVERT: J 36 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8894 (p0) REVERT: J 135 ASP cc_start: 0.8752 (t0) cc_final: 0.8445 (t0) REVERT: J 301 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7720 (p0) REVERT: J 304 LYS cc_start: 0.9033 (pptt) cc_final: 0.8773 (pptt) REVERT: J 305 LEU cc_start: 0.9193 (mt) cc_final: 0.8813 (mt) REVERT: J 314 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7306 (tmm160) REVERT: J 322 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8204 (mtmt) REVERT: J 324 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8691 (tt) REVERT: K 23 MET cc_start: 0.8919 (tpp) cc_final: 0.8297 (tpt) REVERT: K 135 ASP cc_start: 0.8542 (t0) cc_final: 0.7944 (t0) REVERT: K 181 GLN cc_start: 0.8646 (tt0) cc_final: 0.8362 (tp-100) REVERT: K 311 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7496 (tp30) REVERT: L 23 MET cc_start: 0.7727 (tmm) cc_final: 0.7154 (tpt) outliers start: 119 outliers final: 99 residues processed: 451 average time/residue: 0.3428 time to fit residues: 240.9432 Evaluate side-chains 453 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 345 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 124 LYS Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 SER 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 100 ASP Chi-restraints excluded: chain C residue 127 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 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 229 SER 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 118 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 36 ASP 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 291 ASP 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 202 ILE Chi-restraints excluded: chain H residue 20 TYR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 325 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 36 ASP 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 164 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 323 SER Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 358 VAL Chi-restraints excluded: chain K residue 104 THR 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 331 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 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 360 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 3.9990 chunk 215 optimal weight: 0.0060 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 chunk 234 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 181 GLN K 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.126127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.089170 restraints weight = 47927.008| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.49 r_work: 0.3124 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 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 = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24758 Z= 0.157 Angle : 0.517 8.418 33574 Z= 0.256 Chirality : 0.038 0.208 3830 Planarity : 0.003 0.034 4246 Dihedral : 4.599 79.495 3407 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.04 % Allowed : 30.90 % Favored : 65.06 % 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: 2.39 (0.16), residues: 2944 helix: 2.50 (0.12), residues: 1951 sheet: 1.08 (0.32), residues: 326 loop : -1.02 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 16 HIS 0.004 0.001 HIS F 101 PHE 0.029 0.001 PHE G 298 TYR 0.022 0.001 TYR D 194 ARG 0.006 0.000 ARG K 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5908.78 seconds wall clock time: 104 minutes 56.06 seconds (6296.06 seconds total)