Starting phenix.real_space_refine on Mon May 26 17:30:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zby_11158/05_2025/6zby_11158.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zby_11158/05_2025/6zby_11158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zby_11158/05_2025/6zby_11158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zby_11158/05_2025/6zby_11158.map" model { file = "/net/cci-nas-00/data/ceres_data/6zby_11158/05_2025/6zby_11158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zby_11158/05_2025/6zby_11158.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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 18432 2.51 5 N 4944 2.21 5 O 5316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 197 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28836 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "B" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "C" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "D" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "E" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "F" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "G" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "H" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "I" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "J" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "K" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "L" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Time building chain proxies: 16.32, per 1000 atoms: 0.57 Number of scatterers: 28836 At special positions: 0 Unit cell: (143.576, 141.48, 158.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 5316 8.00 N 4944 7.00 C 18432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.00 Conformation dependent library (CDL) restraints added in 3.6 seconds 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6936 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 38 sheets defined 37.7% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'A' and resid 21 through 39 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.679A pdb=" N LEU A 60 " --> pdb=" O TRP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 removed outlier: 4.921A pdb=" N ARG A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 94 removed outlier: 4.317A pdb=" N LEU A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.516A pdb=" N ARG A 138 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.584A pdb=" N LEU A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 202 through 218 Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'B' and resid 21 through 39 removed outlier: 3.827A pdb=" N ALA B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 66 through 76 removed outlier: 4.409A pdb=" N GLN B 71 " --> pdb=" O MET B 67 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARG B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 removed outlier: 3.564A pdb=" N LEU B 88 " --> pdb=" O PRO B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 139 Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.626A pdb=" N ASP B 148 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 removed outlier: 3.873A pdb=" N GLN B 169 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 4.444A pdb=" N MET B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 202 through 218 removed outlier: 3.584A pdb=" N ASN B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 4.123A pdb=" N GLU B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'C' and resid 21 through 39 Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.600A pdb=" N LEU C 60 " --> pdb=" O TRP C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 77 removed outlier: 5.079A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N PHE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN C 71 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.962A pdb=" N LEU C 88 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 93 " --> pdb=" O CYS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 169 through 178 removed outlier: 3.998A pdb=" N MET C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.552A pdb=" N LEU C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 201' Processing helix chain 'C' and resid 202 through 218 Processing helix chain 'C' and resid 229 through 234 removed outlier: 3.512A pdb=" N LEU C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C 234 " --> pdb=" O LYS C 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 234' Processing helix chain 'C' and resid 239 through 246 removed outlier: 4.877A pdb=" N GLU C 244 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 288 removed outlier: 4.025A pdb=" N VAL C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.537A pdb=" N LEU D 60 " --> pdb=" O TRP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 77 removed outlier: 4.742A pdb=" N ARG D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN D 71 " --> pdb=" O MET D 67 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 removed outlier: 4.040A pdb=" N LEU D 88 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 139 Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 169 through 178 removed outlier: 4.266A pdb=" N MET D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 Processing helix chain 'D' and resid 202 through 218 removed outlier: 3.513A pdb=" N ASN D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 234 Processing helix chain 'D' and resid 239 through 244 removed outlier: 4.277A pdb=" N GLU D 244 " --> pdb=" O PRO D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 291 removed outlier: 3.707A pdb=" N ALA D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA D 290 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 39 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 62 through 76 removed outlier: 5.248A pdb=" N ARG E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN E 71 " --> pdb=" O MET E 67 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG E 72 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 96 removed outlier: 3.872A pdb=" N LEU E 88 " --> pdb=" O PRO E 84 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 93 " --> pdb=" O CYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 139 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 165 through 168 Processing helix chain 'E' and resid 169 through 178 removed outlier: 3.713A pdb=" N MET E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 201 Processing helix chain 'E' and resid 202 through 218 Processing helix chain 'E' and resid 229 through 237 removed outlier: 4.084A pdb=" N GLU E 235 " --> pdb=" O GLU E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 244 removed outlier: 3.859A pdb=" N GLU E 244 " --> pdb=" O PRO E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 291 removed outlier: 3.509A pdb=" N ALA E 289 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA E 290 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 39 Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 62 through 76 removed outlier: 4.877A pdb=" N ARG F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N PHE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN F 71 " --> pdb=" O MET F 67 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ARG F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.929A pdb=" N LEU F 88 " --> pdb=" O PRO F 84 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 93 " --> pdb=" O CYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 165 through 168 Processing helix chain 'F' and resid 169 through 178 removed outlier: 3.619A pdb=" N MET F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 201 removed outlier: 3.606A pdb=" N LEU F 201 " --> pdb=" O ALA F 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 198 through 201' Processing helix chain 'F' and resid 202 through 218 Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'F' and resid 239 through 244 removed outlier: 3.506A pdb=" N ALA F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU F 244 " --> pdb=" O PRO F 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 239 through 244' Processing helix chain 'F' and resid 283 through 288 Processing helix chain 'G' and resid 21 through 39 Processing helix chain 'G' and resid 55 through 60 Processing helix chain 'G' and resid 62 through 75 removed outlier: 5.309A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N PHE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN G 71 " --> pdb=" O MET G 67 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ARG G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 96 removed outlier: 3.626A pdb=" N LEU G 88 " --> pdb=" O PRO G 84 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA G 93 " --> pdb=" O CYS G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 139 Processing helix chain 'G' and resid 145 through 149 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 169 through 178 removed outlier: 3.854A pdb=" N MET G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 201 Processing helix chain 'G' and resid 202 through 218 Processing helix chain 'G' and resid 229 through 237 removed outlier: 3.977A pdb=" N GLU G 235 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G 236 " --> pdb=" O MET G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 243 removed outlier: 3.518A pdb=" N LYS G 242 " --> pdb=" O SER G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 291 removed outlier: 4.147A pdb=" N ALA G 290 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR G 291 " --> pdb=" O ALA G 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 39 removed outlier: 3.521A pdb=" N GLU H 39 " --> pdb=" O GLN H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 61 Processing helix chain 'H' and resid 62 through 76 removed outlier: 5.286A pdb=" N ARG H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN H 71 " --> pdb=" O MET H 67 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ARG H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 96 removed outlier: 3.658A pdb=" N LEU H 88 " --> pdb=" O PRO H 84 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA H 93 " --> pdb=" O CYS H 89 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS H 95 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 139 Processing helix chain 'H' and resid 145 through 149 Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'H' and resid 169 through 178 Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.617A pdb=" N LEU H 201 " --> pdb=" O ALA H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 202 through 218 Processing helix chain 'H' and resid 229 through 234 Processing helix chain 'H' and resid 239 through 243 removed outlier: 3.577A pdb=" N LYS H 242 " --> pdb=" O SER H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 291 removed outlier: 3.506A pdb=" N ALA H 289 " --> pdb=" O GLY H 285 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA H 290 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 291 " --> pdb=" O ALA H 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 39 Processing helix chain 'I' and resid 56 through 61 Processing helix chain 'I' and resid 62 through 76 removed outlier: 5.297A pdb=" N ARG I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N PHE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN I 71 " --> pdb=" O MET I 67 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 96 removed outlier: 3.726A pdb=" N LEU I 88 " --> pdb=" O PRO I 84 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA I 93 " --> pdb=" O CYS I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 140 Processing helix chain 'I' and resid 145 through 149 Processing helix chain 'I' and resid 165 through 167 No H-bonds generated for 'chain 'I' and resid 165 through 167' Processing helix chain 'I' and resid 169 through 178 removed outlier: 3.689A pdb=" N MET I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 201 Processing helix chain 'I' and resid 202 through 218 Processing helix chain 'I' and resid 229 through 234 Processing helix chain 'I' and resid 239 through 244 Processing helix chain 'I' and resid 283 through 291 removed outlier: 3.634A pdb=" N ALA I 289 " --> pdb=" O GLY I 285 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA I 290 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR I 291 " --> pdb=" O ALA I 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 39 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'J' and resid 62 through 76 removed outlier: 5.076A pdb=" N ARG J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N PHE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN J 71 " --> pdb=" O MET J 67 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ARG J 72 " --> pdb=" O ARG J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 96 removed outlier: 3.761A pdb=" N LEU J 88 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 139 Processing helix chain 'J' and resid 145 through 149 Processing helix chain 'J' and resid 165 through 168 Processing helix chain 'J' and resid 169 through 178 removed outlier: 3.737A pdb=" N MET J 176 " --> pdb=" O SER J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 201 removed outlier: 3.652A pdb=" N LEU J 201 " --> pdb=" O ALA J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 198 through 201' Processing helix chain 'J' and resid 202 through 218 Processing helix chain 'J' and resid 229 through 237 removed outlier: 3.625A pdb=" N GLU J 235 " --> pdb=" O GLU J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 244 removed outlier: 3.556A pdb=" N GLU J 244 " --> pdb=" O PRO J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 291 removed outlier: 4.075A pdb=" N ALA J 290 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR J 291 " --> pdb=" O ALA J 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 40 Processing helix chain 'K' and resid 56 through 61 Processing helix chain 'K' and resid 62 through 76 removed outlier: 5.362A pdb=" N ARG K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE K 69 " --> pdb=" O GLY K 65 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN K 71 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG K 72 " --> pdb=" O ARG K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 96 removed outlier: 3.639A pdb=" N LEU K 88 " --> pdb=" O PRO K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 139 Processing helix chain 'K' and resid 145 through 149 removed outlier: 3.604A pdb=" N LEU K 149 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 168 Processing helix chain 'K' and resid 169 through 178 removed outlier: 3.807A pdb=" N MET K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 201 Processing helix chain 'K' and resid 202 through 218 removed outlier: 3.502A pdb=" N ASN K 206 " --> pdb=" O SER K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 234 Processing helix chain 'K' and resid 239 through 244 removed outlier: 4.096A pdb=" N GLU K 244 " --> pdb=" O PRO K 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 288 removed outlier: 4.111A pdb=" N VAL K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 39 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.639A pdb=" N LEU L 60 " --> pdb=" O TRP L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 76 removed outlier: 4.843A pdb=" N ARG L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N PHE L 69 " --> pdb=" O GLY L 65 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN L 71 " --> pdb=" O MET L 67 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG L 72 " --> pdb=" O ARG L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 removed outlier: 4.036A pdb=" N LEU L 88 " --> pdb=" O PRO L 84 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA L 93 " --> pdb=" O CYS L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 140 Processing helix chain 'L' and resid 145 through 149 Processing helix chain 'L' and resid 165 through 168 Processing helix chain 'L' and resid 169 through 178 removed outlier: 3.685A pdb=" N MET L 176 " --> pdb=" O SER L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 201 Processing helix chain 'L' and resid 202 through 218 Processing helix chain 'L' and resid 229 through 234 removed outlier: 3.922A pdb=" N ASP L 234 " --> pdb=" O LYS L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 246 removed outlier: 5.224A pdb=" N GLU L 244 " --> pdb=" O ALA L 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU L 246 " --> pdb=" O ALA L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 288 removed outlier: 4.067A pdb=" N VAL L 286 " --> pdb=" O GLY L 282 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 129 removed outlier: 6.891A pdb=" N ILE A 117 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR A 127 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN A 115 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 129 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 113 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER A 42 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS A 9 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 44 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA A 11 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A 225 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 15 " --> pdb=" O CYS A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 129 removed outlier: 6.891A pdb=" N ILE A 117 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR A 127 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN A 115 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 129 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 113 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER A 42 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS A 9 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 44 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA A 11 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 154 removed outlier: 6.288A pdb=" N ARG A 158 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE A 185 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY A 160 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA A 187 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 162 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 315 through 317 removed outlier: 8.444A pdb=" N HIS D 316 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 305 " --> pdb=" O HIS D 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 129 removed outlier: 6.624A pdb=" N LEU B 111 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 129 removed outlier: 6.868A pdb=" N VAL B 44 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY B 102 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 43 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 154 removed outlier: 6.495A pdb=" N ARG B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE B 185 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY B 160 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA B 187 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 162 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS B 184 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 124 through 129 removed outlier: 7.005A pdb=" N ILE C 117 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR C 127 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN C 115 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG C 129 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU C 113 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C 44 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLY C 102 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 43 " --> pdb=" O LYS C 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AB1, first strand: chain 'C' and resid 315 through 317 removed outlier: 6.243A pdb=" N HIS C 316 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N HIS F 316 " --> pdb=" O LEU D 303 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU D 305 " --> pdb=" O HIS F 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 124 through 129 removed outlier: 6.613A pdb=" N ILE D 117 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR D 127 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN D 115 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG D 129 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU D 113 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU D 111 " --> pdb=" O GLY D 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 124 through 129 removed outlier: 6.613A pdb=" N ILE D 117 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR D 127 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN D 115 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG D 129 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU D 113 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER D 42 " --> pdb=" O TYR D 98 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL D 100 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL D 44 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLY D 102 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N SER D 42 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LYS D 9 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL D 44 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA D 11 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 152 through 154 removed outlier: 6.257A pdb=" N ARG D 158 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE D 185 " --> pdb=" O ARG D 158 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLY D 160 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA D 187 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU D 162 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 124 through 129 removed outlier: 7.169A pdb=" N LEU E 111 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 124 through 129 removed outlier: 3.652A pdb=" N THR E 110 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N ALA E 41 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS E 9 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU E 43 " --> pdb=" O LYS E 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 151 through 154 removed outlier: 6.337A pdb=" N ARG E 158 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE E 185 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY E 160 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA E 187 " --> pdb=" O GLY E 160 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU E 162 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 315 through 317 Processing sheet with id=AB9, first strand: chain 'F' and resid 124 through 129 removed outlier: 7.241A pdb=" N LEU F 111 " --> pdb=" O GLY F 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 124 through 129 removed outlier: 8.191A pdb=" N SER F 42 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LYS F 9 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL F 44 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA F 11 " --> pdb=" O VAL F 44 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 151 through 154 Processing sheet with id=AC3, first strand: chain 'G' and resid 124 through 129 removed outlier: 6.892A pdb=" N ILE G 117 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR G 127 " --> pdb=" O GLN G 115 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN G 115 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG G 129 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU G 113 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N SER G 42 " --> pdb=" O GLN G 7 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS G 9 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL G 44 " --> pdb=" O LYS G 9 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA G 11 " --> pdb=" O VAL G 44 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N CYS G 225 " --> pdb=" O ALA G 11 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL G 13 " --> pdb=" O CYS G 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 141 through 142 removed outlier: 7.054A pdb=" N LEU G 111 " --> pdb=" O GLY G 142 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N SER G 42 " --> pdb=" O GLN G 7 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS G 9 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL G 44 " --> pdb=" O LYS G 9 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA G 11 " --> pdb=" O VAL G 44 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 159 through 163 removed outlier: 7.003A pdb=" N GLY G 160 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA G 187 " --> pdb=" O GLY G 160 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU G 162 " --> pdb=" O ALA G 187 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 315 through 317 removed outlier: 6.333A pdb=" N HIS G 316 " --> pdb=" O VAL I 307 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N HIS J 316 " --> pdb=" O LEU H 303 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU H 305 " --> pdb=" O HIS J 316 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 124 through 129 removed outlier: 7.954A pdb=" N SER H 42 " --> pdb=" O GLN H 7 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LYS H 9 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL H 44 " --> pdb=" O LYS H 9 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA H 11 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N CYS H 225 " --> pdb=" O ALA H 11 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL H 13 " --> pdb=" O CYS H 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 141 through 142 removed outlier: 7.118A pdb=" N LEU H 111 " --> pdb=" O GLY H 142 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N SER H 42 " --> pdb=" O GLN H 7 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LYS H 9 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL H 44 " --> pdb=" O LYS H 9 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA H 11 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 151 through 152 removed outlier: 7.107A pdb=" N GLY H 160 " --> pdb=" O ILE H 185 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA H 187 " --> pdb=" O GLY H 160 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU H 162 " --> pdb=" O ALA H 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 124 through 129 removed outlier: 6.703A pdb=" N SER I 42 " --> pdb=" O TYR I 98 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL I 100 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL I 44 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY I 102 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER I 42 " --> pdb=" O GLN I 7 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LYS I 9 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL I 44 " --> pdb=" O LYS I 9 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA I 11 " --> pdb=" O VAL I 44 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 151 through 152 Processing sheet with id=AD3, first strand: chain 'I' and resid 315 through 317 removed outlier: 8.339A pdb=" N HIS L 316 " --> pdb=" O LEU J 303 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU J 305 " --> pdb=" O HIS L 316 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 124 through 129 removed outlier: 6.722A pdb=" N ILE J 117 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR J 127 " --> pdb=" O GLN J 115 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN J 115 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG J 129 " --> pdb=" O LEU J 113 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU J 113 " --> pdb=" O ARG J 129 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU J 111 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 124 through 129 removed outlier: 6.722A pdb=" N ILE J 117 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR J 127 " --> pdb=" O GLN J 115 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN J 115 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG J 129 " --> pdb=" O LEU J 113 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU J 113 " --> pdb=" O ARG J 129 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER J 42 " --> pdb=" O GLN J 7 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS J 9 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL J 44 " --> pdb=" O LYS J 9 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA J 11 " --> pdb=" O VAL J 44 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 151 through 154 removed outlier: 6.470A pdb=" N ARG J 158 " --> pdb=" O VAL J 183 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ILE J 185 " --> pdb=" O ARG J 158 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY J 160 " --> pdb=" O ILE J 185 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA J 187 " --> pdb=" O GLY J 160 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU J 162 " --> pdb=" O ALA J 187 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 124 through 129 removed outlier: 6.717A pdb=" N ILE K 117 " --> pdb=" O VAL K 125 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN K 115 " --> pdb=" O THR K 127 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG K 129 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU K 113 " --> pdb=" O ARG K 129 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR K 110 " --> pdb=" O SER K 107 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER K 42 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL K 100 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL K 44 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY K 102 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N SER K 42 " --> pdb=" O GLN K 7 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS K 9 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL K 44 " --> pdb=" O LYS K 9 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA K 11 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N CYS K 225 " --> pdb=" O ALA K 11 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL K 13 " --> pdb=" O CYS K 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 141 through 142 removed outlier: 7.249A pdb=" N LEU K 111 " --> pdb=" O GLY K 142 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR K 110 " --> pdb=" O SER K 107 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER K 42 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL K 100 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL K 44 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY K 102 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N SER K 42 " --> pdb=" O GLN K 7 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS K 9 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL K 44 " --> pdb=" O LYS K 9 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA K 11 " --> pdb=" O VAL K 44 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 151 through 154 removed outlier: 6.484A pdb=" N HIS K 184 " --> pdb=" O LEU K 222 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 124 through 129 removed outlier: 6.984A pdb=" N ILE L 117 " --> pdb=" O VAL L 125 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR L 127 " --> pdb=" O GLN L 115 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN L 115 " --> pdb=" O THR L 127 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG L 129 " --> pdb=" O LEU L 113 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU L 113 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU L 43 " --> pdb=" O LYS L 9 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 151 through 154 1232 hydrogen bonds defined for protein. 3282 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: 10.51 Time building geometry restraints manager: 8.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6222 1.32 - 1.45: 6837 1.45 - 1.58: 16278 1.58 - 1.70: 3 1.70 - 1.83: 204 Bond restraints: 29544 Sorted by residual: bond pdb=" CZ ARG H 309 " pdb=" NH2 ARG H 309 " ideal model delta sigma weight residual 1.330 1.273 0.057 1.30e-02 5.92e+03 1.95e+01 bond pdb=" CB THR K 313 " pdb=" OG1 THR K 313 " ideal model delta sigma weight residual 1.433 1.365 0.068 1.60e-02 3.91e+03 1.83e+01 bond pdb=" CZ ARG A 87 " pdb=" NH2 ARG A 87 " ideal model delta sigma weight residual 1.330 1.279 0.051 1.30e-02 5.92e+03 1.55e+01 bond pdb=" CZ ARG J 314 " pdb=" NH2 ARG J 314 " ideal model delta sigma weight residual 1.330 1.279 0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" N ILE E 237 " pdb=" CA ILE E 237 " ideal model delta sigma weight residual 1.456 1.501 -0.044 1.14e-02 7.69e+03 1.51e+01 ... (remaining 29539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 39571 4.94 - 9.88: 642 9.88 - 14.82: 6 14.82 - 19.77: 7 19.77 - 24.71: 10 Bond angle restraints: 40236 Sorted by residual: angle pdb=" CA ILE E 237 " pdb=" CB ILE E 237 " pdb=" CG1 ILE E 237 " ideal model delta sigma weight residual 110.40 135.11 -24.71 1.70e+00 3.46e-01 2.11e+02 angle pdb=" CA VAL A 124 " pdb=" CB VAL A 124 " pdb=" CG1 VAL A 124 " ideal model delta sigma weight residual 110.40 133.98 -23.58 1.70e+00 3.46e-01 1.92e+02 angle pdb=" CA THR F 265 " pdb=" CB THR F 265 " pdb=" OG1 THR F 265 " ideal model delta sigma weight residual 109.60 128.39 -18.79 1.50e+00 4.44e-01 1.57e+02 angle pdb=" CA VAL L 124 " pdb=" CB VAL L 124 " pdb=" CG1 VAL L 124 " ideal model delta sigma weight residual 110.40 131.69 -21.29 1.70e+00 3.46e-01 1.57e+02 angle pdb=" CA VAL A 80 " pdb=" CB VAL A 80 " pdb=" CG1 VAL A 80 " ideal model delta sigma weight residual 110.40 131.63 -21.23 1.70e+00 3.46e-01 1.56e+02 ... (remaining 40231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.22: 16078 18.22 - 36.44: 1036 36.44 - 54.66: 258 54.66 - 72.88: 80 72.88 - 91.10: 32 Dihedral angle restraints: 17484 sinusoidal: 6600 harmonic: 10884 Sorted by residual: dihedral pdb=" N PRO I 240 " pdb=" C PRO I 240 " pdb=" CA PRO I 240 " pdb=" CB PRO I 240 " ideal model delta harmonic sigma weight residual 115.10 143.19 -28.09 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" C PRO I 240 " pdb=" N PRO I 240 " pdb=" CA PRO I 240 " pdb=" CB PRO I 240 " ideal model delta harmonic sigma weight residual -120.70 -145.76 25.06 0 2.50e+00 1.60e-01 1.00e+02 dihedral pdb=" C GLN B 319 " pdb=" N GLN B 319 " pdb=" CA GLN B 319 " pdb=" CB GLN B 319 " ideal model delta harmonic sigma weight residual -122.60 -144.48 21.88 0 2.50e+00 1.60e-01 7.66e+01 ... (remaining 17481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 4295 0.256 - 0.513: 102 0.513 - 0.769: 16 0.769 - 1.025: 12 1.025 - 1.282: 3 Chirality restraints: 4428 Sorted by residual: chirality pdb=" CB VAL L 124 " pdb=" CA VAL L 124 " pdb=" CG1 VAL L 124 " pdb=" CG2 VAL L 124 " both_signs ideal model delta sigma weight residual False -2.63 -1.35 -1.28 2.00e-01 2.50e+01 4.11e+01 chirality pdb=" CA PRO I 240 " pdb=" N PRO I 240 " pdb=" C PRO I 240 " pdb=" CB PRO I 240 " both_signs ideal model delta sigma weight residual False 2.72 1.48 1.23 2.00e-01 2.50e+01 3.81e+01 chirality pdb=" CB VAL A 124 " pdb=" CA VAL A 124 " pdb=" CG1 VAL A 124 " pdb=" CG2 VAL A 124 " both_signs ideal model delta sigma weight residual False -2.63 -1.42 -1.21 2.00e-01 2.50e+01 3.65e+01 ... (remaining 4425 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 297 " 0.281 2.00e-02 2.50e+03 1.54e-01 4.74e+02 pdb=" CG TYR B 297 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR B 297 " -0.150 2.00e-02 2.50e+03 pdb=" CD2 TYR B 297 " -0.137 2.00e-02 2.50e+03 pdb=" CE1 TYR B 297 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 TYR B 297 " -0.097 2.00e-02 2.50e+03 pdb=" CZ TYR B 297 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 297 " 0.225 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 297 " 0.237 2.00e-02 2.50e+03 1.37e-01 3.73e+02 pdb=" CG TYR K 297 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR K 297 " -0.136 2.00e-02 2.50e+03 pdb=" CD2 TYR K 297 " -0.097 2.00e-02 2.50e+03 pdb=" CE1 TYR K 297 " -0.065 2.00e-02 2.50e+03 pdb=" CE2 TYR K 297 " -0.109 2.00e-02 2.50e+03 pdb=" CZ TYR K 297 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR K 297 " 0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 297 " -0.234 2.00e-02 2.50e+03 1.34e-01 3.60e+02 pdb=" CG TYR D 297 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR D 297 " 0.123 2.00e-02 2.50e+03 pdb=" CD2 TYR D 297 " 0.116 2.00e-02 2.50e+03 pdb=" CE1 TYR D 297 " 0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR D 297 " 0.090 2.00e-02 2.50e+03 pdb=" CZ TYR D 297 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 297 " -0.212 2.00e-02 2.50e+03 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 13591 2.99 - 3.47: 29215 3.47 - 3.95: 53311 3.95 - 4.42: 62361 4.42 - 4.90: 98577 Nonbonded interactions: 257055 Sorted by model distance: nonbonded pdb=" OD1 ASP J 145 " pdb=" OG SER J 147 " model vdw 2.514 3.040 nonbonded pdb=" OD1 ASP E 145 " pdb=" OG SER E 147 " model vdw 2.532 3.040 nonbonded pdb=" OD1 ASP G 145 " pdb=" OG SER G 147 " model vdw 2.536 3.040 nonbonded pdb=" OD1 ASP D 145 " pdb=" OG SER D 147 " model vdw 2.543 3.040 nonbonded pdb=" OD1 ASP I 145 " pdb=" OG SER I 147 " model vdw 2.544 3.040 ... (remaining 257050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 61.340 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.140 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.013 0.068 29544 Z= 0.787 Angle : 2.021 24.707 40236 Z= 1.336 Chirality : 0.125 1.282 4428 Planarity : 0.017 0.154 5268 Dihedral : 14.555 91.098 10548 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.30 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 4.15 % Favored : 94.61 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 5.56 % 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 (0.13), residues: 3768 helix: -2.51 (0.11), residues: 1188 sheet: -1.49 (0.17), residues: 840 loop : -0.62 (0.16), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.138 0.031 TRP I 56 HIS 0.022 0.005 HIS F 135 PHE 0.088 0.020 PHE D 252 TYR 0.281 0.027 TYR B 297 ARG 0.019 0.002 ARG D 138 Details of bonding type rmsd hydrogen bonds : bond 0.18832 ( 1169) hydrogen bonds : angle 8.86212 ( 3282) covalent geometry : bond 0.01252 (29544) covalent geometry : angle 2.02108 (40236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 667 time to evaluate : 3.036 Fit side-chains REVERT: A 75 ASP cc_start: 0.7213 (m-30) cc_final: 0.6959 (m-30) REVERT: A 120 ASP cc_start: 0.6325 (m-30) cc_final: 0.6075 (m-30) REVERT: A 131 LEU cc_start: 0.8646 (mp) cc_final: 0.8362 (mt) REVERT: A 143 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6314 (tt0) REVERT: A 148 ASP cc_start: 0.7736 (m-30) cc_final: 0.7434 (m-30) REVERT: A 247 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6840 (mt) REVERT: A 312 MET cc_start: 0.7151 (mtt) cc_final: 0.6822 (mtm) REVERT: B 80 VAL cc_start: 0.6819 (t) cc_final: 0.6561 (m) REVERT: B 163 CYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7221 (m) REVERT: B 166 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7673 (mt-10) REVERT: B 206 ASN cc_start: 0.8267 (m-40) cc_final: 0.7873 (m-40) REVERT: C 96 LYS cc_start: 0.7058 (tppt) cc_final: 0.6837 (tptt) REVERT: C 218 GLN cc_start: 0.8215 (mp10) cc_final: 0.7790 (mp10) REVERT: D 21 ASP cc_start: 0.7632 (t0) cc_final: 0.7409 (t0) REVERT: D 50 TRP cc_start: 0.8343 (t60) cc_final: 0.8084 (t60) REVERT: D 76 ASN cc_start: 0.8486 (m110) cc_final: 0.7929 (m110) REVERT: D 79 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6194 (mt-10) REVERT: D 90 ARG cc_start: 0.7379 (mmt90) cc_final: 0.7005 (mmp-170) REVERT: D 182 GLN cc_start: 0.7776 (mt0) cc_final: 0.7485 (mt0) REVERT: D 254 MET cc_start: 0.8414 (mmt) cc_final: 0.8109 (mmp) REVERT: E 71 GLN cc_start: 0.7842 (tt0) cc_final: 0.7329 (tt0) REVERT: E 75 ASP cc_start: 0.7516 (m-30) cc_final: 0.7247 (m-30) REVERT: E 168 ILE cc_start: 0.8445 (mm) cc_final: 0.8126 (mt) REVERT: E 309 ARG cc_start: 0.7416 (mtm180) cc_final: 0.7150 (mmm-85) REVERT: F 76 ASN cc_start: 0.8836 (m110) cc_final: 0.8620 (m110) REVERT: F 135 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7290 (p-80) REVERT: F 176 MET cc_start: 0.8799 (mmm) cc_final: 0.8484 (mmm) REVERT: G 135 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.7536 (p-80) REVERT: H 35 GLN cc_start: 0.8183 (tt0) cc_final: 0.7981 (tt0) REVERT: H 71 GLN cc_start: 0.7525 (tt0) cc_final: 0.7150 (tt0) REVERT: H 96 LYS cc_start: 0.6960 (mmtt) cc_final: 0.6298 (mptt) REVERT: H 176 MET cc_start: 0.8752 (mmm) cc_final: 0.8548 (mmp) REVERT: I 135 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7472 (p-80) REVERT: J 309 ARG cc_start: 0.7208 (mtm180) cc_final: 0.6821 (mmm-85) REVERT: K 6 LYS cc_start: 0.8148 (mttp) cc_final: 0.7851 (mttm) REVERT: K 76 ASN cc_start: 0.8313 (m110) cc_final: 0.7938 (m110) REVERT: K 90 ARG cc_start: 0.7297 (mmt90) cc_final: 0.7003 (mmp-170) REVERT: K 254 MET cc_start: 0.8460 (mmt) cc_final: 0.8183 (mmp) REVERT: L 51 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8238 (mt) REVERT: L 304 ARG cc_start: 0.8115 (mtt180) cc_final: 0.6890 (ttt180) REVERT: L 309 ARG cc_start: 0.6222 (mtm180) cc_final: 0.5484 (mtm180) outliers start: 36 outliers final: 9 residues processed: 681 average time/residue: 0.4323 time to fit residues: 452.0662 Evaluate side-chains 467 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 452 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain F residue 135 HIS Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain G residue 135 HIS Chi-restraints excluded: chain I residue 135 HIS Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 124 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 291 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 337 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 207 ASN B 135 HIS B 179 GLN B 200 GLN C 71 GLN C 115 GLN C 169 GLN D 76 ASN D 135 HIS E 115 GLN E 135 HIS E 316 HIS F 169 GLN G 76 ASN ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 GLN G 316 HIS H 316 HIS I 71 GLN I 76 ASN I 169 GLN I 207 ASN J 76 ASN J 115 GLN J 135 HIS J 316 HIS K 115 GLN K 135 HIS K 169 GLN L 135 HIS L 204 GLN L 319 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.122835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.093917 restraints weight = 36527.681| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.51 r_work: 0.2820 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 29544 Z= 0.198 Angle : 0.679 8.944 40236 Z= 0.355 Chirality : 0.046 0.221 4428 Planarity : 0.005 0.061 5268 Dihedral : 6.289 40.104 4150 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.35 % Allowed : 1.78 % Favored : 97.88 % Rotamer: Outliers : 1.31 % Allowed : 8.26 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.36 (0.14), residues: 3768 helix: -1.30 (0.13), residues: 1308 sheet: -1.21 (0.18), residues: 780 loop : -0.14 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 50 HIS 0.006 0.001 HIS F 152 PHE 0.014 0.002 PHE G 69 TYR 0.017 0.002 TYR E 317 ARG 0.006 0.001 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 1169) hydrogen bonds : angle 5.92681 ( 3282) covalent geometry : bond 0.00461 (29544) covalent geometry : angle 0.67867 (40236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 528 time to evaluate : 2.909 Fit side-chains revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7570 (m-80) cc_final: 0.7364 (m-80) REVERT: A 131 LEU cc_start: 0.8500 (mp) cc_final: 0.8083 (mt) REVERT: A 143 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7095 (mt-10) REVERT: A 248 GLU cc_start: 0.6432 (tp30) cc_final: 0.5996 (tp30) REVERT: A 301 ASP cc_start: 0.7272 (m-30) cc_final: 0.6066 (t70) REVERT: A 312 MET cc_start: 0.7577 (mtt) cc_final: 0.7192 (mtt) REVERT: B 86 GLU cc_start: 0.4442 (mm-30) cc_final: 0.4182 (tt0) REVERT: B 190 SER cc_start: 0.8587 (m) cc_final: 0.8282 (p) REVERT: B 271 GLU cc_start: 0.7123 (tt0) cc_final: 0.6401 (mt-10) REVERT: B 314 ARG cc_start: 0.7674 (mpt180) cc_final: 0.7281 (mmt-90) REVERT: C 96 LYS cc_start: 0.6881 (tppt) cc_final: 0.6606 (tptt) REVERT: C 123 ARG cc_start: 0.6527 (ptp-170) cc_final: 0.6162 (ptp90) REVERT: C 304 ARG cc_start: 0.8584 (mtt180) cc_final: 0.8367 (mtt180) REVERT: D 50 TRP cc_start: 0.8549 (t60) cc_final: 0.8162 (t60) REVERT: D 76 ASN cc_start: 0.8488 (m-40) cc_final: 0.7890 (m110) REVERT: D 90 ARG cc_start: 0.7362 (mmt90) cc_final: 0.6263 (mmp-170) REVERT: D 94 GLN cc_start: 0.7526 (tt0) cc_final: 0.7007 (mt0) REVERT: D 231 GLU cc_start: 0.7136 (pm20) cc_final: 0.6932 (pm20) REVERT: D 254 MET cc_start: 0.8712 (mmt) cc_final: 0.8248 (mmp) REVERT: E 23 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7618 (mm-30) REVERT: E 90 ARG cc_start: 0.6677 (mmp-170) cc_final: 0.5600 (mtm110) REVERT: E 168 ILE cc_start: 0.8714 (mm) cc_final: 0.8475 (mm) REVERT: E 309 ARG cc_start: 0.8031 (mtm180) cc_final: 0.7118 (mtp180) REVERT: F 21 ASP cc_start: 0.7545 (t0) cc_final: 0.7307 (t70) REVERT: F 61 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: G 6 LYS cc_start: 0.7868 (mttp) cc_final: 0.7392 (mtmt) REVERT: G 71 GLN cc_start: 0.8099 (tt0) cc_final: 0.7817 (tp40) REVERT: G 96 LYS cc_start: 0.7510 (mmtt) cc_final: 0.6684 (mptt) REVERT: G 123 ARG cc_start: 0.7999 (ptt-90) cc_final: 0.7540 (ptp90) REVERT: G 145 ASP cc_start: 0.8673 (p0) cc_final: 0.8443 (p0) REVERT: G 271 GLU cc_start: 0.8134 (tp30) cc_final: 0.7875 (tp30) REVERT: H 21 ASP cc_start: 0.8201 (t70) cc_final: 0.7966 (t70) REVERT: H 96 LYS cc_start: 0.7572 (mmtt) cc_final: 0.6799 (mptt) REVERT: H 123 ARG cc_start: 0.7928 (ptt180) cc_final: 0.7601 (ptt-90) REVERT: H 176 MET cc_start: 0.9198 (mmm) cc_final: 0.8745 (mmt) REVERT: I 23 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8140 (mm-30) REVERT: I 271 GLU cc_start: 0.7946 (tp30) cc_final: 0.7429 (mm-30) REVERT: J 76 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8560 (m110) REVERT: J 123 ARG cc_start: 0.7672 (ptt-90) cc_final: 0.7356 (ptt-90) REVERT: J 244 GLU cc_start: 0.8120 (tt0) cc_final: 0.7697 (tp30) REVERT: J 309 ARG cc_start: 0.7906 (mtm180) cc_final: 0.6885 (mmm-85) REVERT: K 6 LYS cc_start: 0.8260 (mttp) cc_final: 0.7814 (mttm) REVERT: K 21 ASP cc_start: 0.8169 (t0) cc_final: 0.7931 (t0) REVERT: K 71 GLN cc_start: 0.8091 (tp40) cc_final: 0.7859 (tt0) REVERT: K 72 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7394 (mtp180) REVERT: K 76 ASN cc_start: 0.8557 (m110) cc_final: 0.7955 (m110) REVERT: K 90 ARG cc_start: 0.7185 (mmt90) cc_final: 0.6219 (mmp-170) REVERT: K 254 MET cc_start: 0.8671 (mmt) cc_final: 0.8228 (mmp) REVERT: K 317 TYR cc_start: 0.8056 (m-80) cc_final: 0.7307 (m-80) REVERT: L 123 ARG cc_start: 0.5961 (ptt180) cc_final: 0.5687 (ptp90) REVERT: L 143 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7815 (mt-10) REVERT: L 169 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7421 (mm-40) REVERT: L 304 ARG cc_start: 0.8610 (mtt180) cc_final: 0.7033 (ttt180) REVERT: L 309 ARG cc_start: 0.6518 (mtm180) cc_final: 0.5781 (mtm180) outliers start: 38 outliers final: 21 residues processed: 543 average time/residue: 0.4416 time to fit residues: 369.0639 Evaluate side-chains 461 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 438 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 207 optimal weight: 7.9990 chunk 88 optimal weight: 0.1980 chunk 369 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 288 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 226 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 256 optimal weight: 10.0000 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 76 ASN C 71 GLN D 14 GLN F 73 ASN F 76 ASN G 76 ASN G 135 HIS G 169 GLN I 73 ASN J 76 ASN K 169 GLN L 207 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.093938 restraints weight = 36754.116| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.49 r_work: 0.2824 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29544 Z= 0.173 Angle : 0.617 8.800 40236 Z= 0.319 Chirality : 0.045 0.195 4428 Planarity : 0.004 0.057 5268 Dihedral : 5.487 36.928 4132 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.44 % Favored : 97.24 % Rotamer: Outliers : 2.01 % Allowed : 10.20 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.05 (0.14), residues: 3768 helix: -0.77 (0.14), residues: 1308 sheet: -1.31 (0.18), residues: 780 loop : -0.06 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 59 HIS 0.005 0.001 HIS B 152 PHE 0.014 0.002 PHE A 69 TYR 0.013 0.001 TYR G 297 ARG 0.005 0.001 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 1169) hydrogen bonds : angle 5.43011 ( 3282) covalent geometry : bond 0.00406 (29544) covalent geometry : angle 0.61725 (40236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 516 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7553 (m-80) cc_final: 0.7297 (m-80) REVERT: A 148 ASP cc_start: 0.7516 (m-30) cc_final: 0.7163 (m-30) REVERT: A 169 GLN cc_start: 0.6349 (mp10) cc_final: 0.5603 (mp10) REVERT: A 236 LEU cc_start: 0.6468 (tp) cc_final: 0.6078 (mt) REVERT: A 312 MET cc_start: 0.7413 (mtt) cc_final: 0.7107 (mtt) REVERT: A 313 THR cc_start: 0.7684 (p) cc_final: 0.7097 (t) REVERT: B 9 LYS cc_start: 0.7267 (ttmt) cc_final: 0.6597 (mtpp) REVERT: B 86 GLU cc_start: 0.4634 (mm-30) cc_final: 0.4313 (tt0) REVERT: B 118 ILE cc_start: 0.7257 (mt) cc_final: 0.6878 (mm) REVERT: B 141 TYR cc_start: 0.8323 (m-80) cc_final: 0.8062 (m-80) REVERT: B 190 SER cc_start: 0.8708 (m) cc_final: 0.8442 (p) REVERT: B 271 GLU cc_start: 0.7014 (tt0) cc_final: 0.6336 (mt-10) REVERT: C 96 LYS cc_start: 0.6819 (tppt) cc_final: 0.6273 (tptm) REVERT: C 272 GLU cc_start: 0.7222 (tt0) cc_final: 0.6955 (mm-30) REVERT: D 76 ASN cc_start: 0.8481 (m-40) cc_final: 0.7836 (m110) REVERT: D 90 ARG cc_start: 0.7214 (mmt90) cc_final: 0.6162 (mmp-170) REVERT: D 94 GLN cc_start: 0.7690 (tt0) cc_final: 0.7019 (mt0) REVERT: E 71 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8119 (tp40) REVERT: E 90 ARG cc_start: 0.6670 (mmp-170) cc_final: 0.5535 (mtt90) REVERT: E 123 ARG cc_start: 0.7523 (ptt-90) cc_final: 0.7074 (ptt-90) REVERT: E 168 ILE cc_start: 0.8590 (mm) cc_final: 0.8316 (mm) REVERT: E 271 GLU cc_start: 0.8168 (tp30) cc_final: 0.7908 (mm-30) REVERT: E 309 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7044 (mtp180) REVERT: F 21 ASP cc_start: 0.7673 (t0) cc_final: 0.7453 (t0) REVERT: G 120 ASP cc_start: 0.7998 (m-30) cc_final: 0.7723 (t0) REVERT: G 271 GLU cc_start: 0.8242 (tp30) cc_final: 0.7968 (tp30) REVERT: H 21 ASP cc_start: 0.8273 (t70) cc_final: 0.8054 (t70) REVERT: H 96 LYS cc_start: 0.7668 (mmtt) cc_final: 0.6960 (mttp) REVERT: H 123 ARG cc_start: 0.7934 (ptt180) cc_final: 0.7585 (ptt-90) REVERT: I 21 ASP cc_start: 0.7655 (t0) cc_final: 0.7268 (t0) REVERT: I 23 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8168 (mm-30) REVERT: I 230 LYS cc_start: 0.8305 (mmtp) cc_final: 0.8078 (mmtt) REVERT: I 271 GLU cc_start: 0.7911 (tp30) cc_final: 0.7424 (mm-30) REVERT: J 39 GLU cc_start: 0.8296 (tp30) cc_final: 0.7962 (tp30) REVERT: J 244 GLU cc_start: 0.8070 (tt0) cc_final: 0.7628 (tp30) REVERT: J 309 ARG cc_start: 0.7820 (mtm180) cc_final: 0.6850 (mmm-85) REVERT: K 6 LYS cc_start: 0.8290 (mttp) cc_final: 0.7848 (mttm) REVERT: K 21 ASP cc_start: 0.8134 (t0) cc_final: 0.7694 (t0) REVERT: K 76 ASN cc_start: 0.8559 (m110) cc_final: 0.7895 (m110) REVERT: K 90 ARG cc_start: 0.7185 (mmt90) cc_final: 0.6207 (mmp-170) REVERT: K 317 TYR cc_start: 0.8079 (m-80) cc_final: 0.7490 (m-80) REVERT: L 123 ARG cc_start: 0.5994 (ptt180) cc_final: 0.5571 (ptp90) REVERT: L 143 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7607 (mt-10) REVERT: L 169 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7778 (mm-40) REVERT: L 272 GLU cc_start: 0.7124 (tt0) cc_final: 0.6820 (mm-30) REVERT: L 304 ARG cc_start: 0.8589 (mtt180) cc_final: 0.7030 (ttt180) REVERT: L 309 ARG cc_start: 0.6655 (mtm180) cc_final: 0.5554 (mtm-85) outliers start: 58 outliers final: 31 residues processed: 547 average time/residue: 0.4303 time to fit residues: 364.5501 Evaluate side-chains 502 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 470 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 131 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 59 optimal weight: 20.0000 chunk 336 optimal weight: 40.0000 chunk 94 optimal weight: 20.0000 chunk 311 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 300 optimal weight: 9.9990 chunk 258 optimal weight: 20.0000 chunk 245 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 339 optimal weight: 8.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 206 ASN B 76 ASN C 71 GLN F 73 ASN F 76 ASN G 135 HIS I 71 GLN I 76 ASN J 76 ASN J 169 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.121515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.092805 restraints weight = 37064.481| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.51 r_work: 0.2798 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29544 Z= 0.187 Angle : 0.613 9.094 40236 Z= 0.316 Chirality : 0.045 0.187 4428 Planarity : 0.004 0.054 5268 Dihedral : 5.334 26.472 4129 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.18 % Favored : 97.51 % Rotamer: Outliers : 2.46 % Allowed : 10.79 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3768 helix: -0.62 (0.14), residues: 1308 sheet: -1.26 (0.17), residues: 828 loop : -0.01 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 59 HIS 0.006 0.001 HIS G 135 PHE 0.012 0.002 PHE A 69 TYR 0.012 0.001 TYR H 174 ARG 0.004 0.000 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 1169) hydrogen bonds : angle 5.35245 ( 3282) covalent geometry : bond 0.00440 (29544) covalent geometry : angle 0.61265 (40236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 485 time to evaluate : 3.414 Fit side-chains REVERT: A 98 TYR cc_start: 0.7591 (m-80) cc_final: 0.7314 (m-80) REVERT: A 143 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7082 (mt-10) REVERT: A 148 ASP cc_start: 0.7460 (m-30) cc_final: 0.7056 (m-30) REVERT: A 169 GLN cc_start: 0.6326 (mp10) cc_final: 0.5501 (mp10) REVERT: A 236 LEU cc_start: 0.6588 (tp) cc_final: 0.6308 (mt) REVERT: A 312 MET cc_start: 0.7373 (mtt) cc_final: 0.7076 (mtt) REVERT: A 313 THR cc_start: 0.7837 (p) cc_final: 0.7306 (t) REVERT: B 9 LYS cc_start: 0.7221 (ttmt) cc_final: 0.6590 (mtpp) REVERT: B 86 GLU cc_start: 0.4640 (mm-30) cc_final: 0.4333 (tt0) REVERT: B 113 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7908 (tp) REVERT: B 118 ILE cc_start: 0.7466 (mt) cc_final: 0.7059 (mm) REVERT: B 141 TYR cc_start: 0.8318 (m-80) cc_final: 0.7915 (m-80) REVERT: B 190 SER cc_start: 0.8697 (m) cc_final: 0.8489 (p) REVERT: C 96 LYS cc_start: 0.6745 (tppt) cc_final: 0.6226 (tptt) REVERT: C 123 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6170 (ptp90) REVERT: D 50 TRP cc_start: 0.8560 (t60) cc_final: 0.8214 (t60) REVERT: D 76 ASN cc_start: 0.8469 (m-40) cc_final: 0.7823 (m110) REVERT: D 90 ARG cc_start: 0.7298 (mmt90) cc_final: 0.6215 (mmp-170) REVERT: D 94 GLN cc_start: 0.7611 (tt0) cc_final: 0.6985 (mt0) REVERT: D 254 MET cc_start: 0.8801 (mmt) cc_final: 0.8548 (mmp) REVERT: D 310 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8043 (mm-30) REVERT: E 23 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7295 (mm-30) REVERT: E 71 GLN cc_start: 0.8388 (tt0) cc_final: 0.7990 (tp40) REVERT: E 90 ARG cc_start: 0.6568 (mmp-170) cc_final: 0.5455 (mtt90) REVERT: E 123 ARG cc_start: 0.7542 (ptt-90) cc_final: 0.7073 (ptt-90) REVERT: E 271 GLU cc_start: 0.8263 (tp30) cc_final: 0.8033 (mm-30) REVERT: E 297 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8547 (t80) REVERT: F 21 ASP cc_start: 0.7689 (t0) cc_final: 0.7148 (t0) REVERT: G 145 ASP cc_start: 0.8289 (p0) cc_final: 0.8035 (p0) REVERT: G 176 MET cc_start: 0.9212 (mmm) cc_final: 0.8948 (mmm) REVERT: G 206 ASN cc_start: 0.8843 (m-40) cc_final: 0.8382 (m-40) REVERT: H 21 ASP cc_start: 0.8285 (t70) cc_final: 0.8028 (t70) REVERT: H 96 LYS cc_start: 0.7693 (mmtt) cc_final: 0.6932 (mptt) REVERT: H 123 ARG cc_start: 0.7976 (ptt180) cc_final: 0.7711 (ptt-90) REVERT: I 21 ASP cc_start: 0.7819 (t0) cc_final: 0.7171 (t0) REVERT: I 23 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8187 (mm-30) REVERT: I 230 LYS cc_start: 0.8353 (mmtp) cc_final: 0.8111 (mmtt) REVERT: I 271 GLU cc_start: 0.7902 (tp30) cc_final: 0.7429 (mm-30) REVERT: J 244 GLU cc_start: 0.8128 (tt0) cc_final: 0.7683 (tp30) REVERT: J 309 ARG cc_start: 0.7645 (mtm180) cc_final: 0.6821 (mtp180) REVERT: K 6 LYS cc_start: 0.8297 (mttp) cc_final: 0.7848 (mttm) REVERT: K 21 ASP cc_start: 0.8206 (t0) cc_final: 0.7727 (t0) REVERT: K 76 ASN cc_start: 0.8601 (m110) cc_final: 0.7957 (m110) REVERT: K 90 ARG cc_start: 0.7175 (mmt90) cc_final: 0.6190 (mmp-170) REVERT: K 317 TYR cc_start: 0.8059 (m-80) cc_final: 0.7551 (m-80) REVERT: L 123 ARG cc_start: 0.6065 (ptt180) cc_final: 0.5664 (ptp90) REVERT: L 169 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7754 (mm-40) REVERT: L 218 GLN cc_start: 0.8445 (mp10) cc_final: 0.7825 (mp10) REVERT: L 272 GLU cc_start: 0.7194 (tt0) cc_final: 0.6936 (mm-30) REVERT: L 304 ARG cc_start: 0.8597 (mtt180) cc_final: 0.7045 (ttt180) REVERT: L 309 ARG cc_start: 0.6570 (mtm180) cc_final: 0.5629 (mtt90) outliers start: 71 outliers final: 51 residues processed: 522 average time/residue: 0.4283 time to fit residues: 347.0686 Evaluate side-chains 516 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 462 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 138 optimal weight: 20.0000 chunk 347 optimal weight: 20.0000 chunk 117 optimal weight: 30.0000 chunk 136 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 28 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 219 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN C 71 GLN F 71 GLN F 73 ASN F 76 ASN F 115 GLN H 115 GLN I 71 GLN I 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.120432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.091644 restraints weight = 36849.316| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.50 r_work: 0.2778 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29544 Z= 0.217 Angle : 0.633 9.113 40236 Z= 0.325 Chirality : 0.046 0.200 4428 Planarity : 0.004 0.057 5268 Dihedral : 5.384 27.188 4129 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.42 % Favored : 97.27 % Rotamer: Outliers : 2.90 % Allowed : 11.27 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3768 helix: -0.59 (0.14), residues: 1308 sheet: -1.36 (0.17), residues: 888 loop : 0.05 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 50 HIS 0.005 0.001 HIS C 135 PHE 0.012 0.002 PHE I 69 TYR 0.014 0.002 TYR E 297 ARG 0.004 0.000 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 1169) hydrogen bonds : angle 5.42739 ( 3282) covalent geometry : bond 0.00512 (29544) covalent geometry : angle 0.63252 (40236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 484 time to evaluate : 3.151 Fit side-chains REVERT: A 143 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7006 (mt-10) REVERT: A 148 ASP cc_start: 0.7526 (m-30) cc_final: 0.7116 (m-30) REVERT: A 169 GLN cc_start: 0.6386 (mp10) cc_final: 0.5475 (mp10) REVERT: A 185 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7815 (mp) REVERT: A 236 LEU cc_start: 0.6472 (tp) cc_final: 0.6231 (mt) REVERT: A 312 MET cc_start: 0.7388 (mtt) cc_final: 0.7124 (mtt) REVERT: A 313 THR cc_start: 0.7706 (p) cc_final: 0.7286 (t) REVERT: B 86 GLU cc_start: 0.4942 (mm-30) cc_final: 0.4589 (tt0) REVERT: B 113 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7947 (tp) REVERT: B 118 ILE cc_start: 0.7217 (mt) cc_final: 0.6816 (mm) REVERT: B 134 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7581 (p) REVERT: B 141 TYR cc_start: 0.8352 (m-80) cc_final: 0.7906 (m-80) REVERT: C 71 GLN cc_start: 0.8116 (tt0) cc_final: 0.7895 (tt0) REVERT: C 96 LYS cc_start: 0.6695 (tppt) cc_final: 0.6174 (tptt) REVERT: C 123 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.6133 (ptp90) REVERT: C 254 MET cc_start: 0.8601 (mmp) cc_final: 0.8395 (mmt) REVERT: D 50 TRP cc_start: 0.8530 (t60) cc_final: 0.8165 (t60) REVERT: D 72 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7381 (mtp180) REVERT: D 76 ASN cc_start: 0.8530 (m-40) cc_final: 0.7875 (m110) REVERT: D 90 ARG cc_start: 0.7221 (mmt90) cc_final: 0.6101 (mmp-170) REVERT: D 94 GLN cc_start: 0.7634 (tt0) cc_final: 0.6930 (mt0) REVERT: D 254 MET cc_start: 0.8815 (mmt) cc_final: 0.8577 (mmp) REVERT: D 310 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7948 (mm-30) REVERT: E 23 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7233 (mm-30) REVERT: E 90 ARG cc_start: 0.6382 (mmp-170) cc_final: 0.5322 (mtt90) REVERT: E 123 ARG cc_start: 0.7530 (ptt-90) cc_final: 0.7064 (ptt-90) REVERT: E 271 GLU cc_start: 0.8227 (tp30) cc_final: 0.7985 (mm-30) REVERT: E 297 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8650 (t80) REVERT: E 312 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8052 (mtm) REVERT: F 21 ASP cc_start: 0.7829 (t0) cc_final: 0.7269 (t0) REVERT: G 121 CYS cc_start: 0.7977 (m) cc_final: 0.7297 (t) REVERT: H 21 ASP cc_start: 0.8308 (t70) cc_final: 0.8034 (t70) REVERT: H 96 LYS cc_start: 0.7627 (mmtt) cc_final: 0.6930 (mptt) REVERT: H 123 ARG cc_start: 0.8020 (ptt180) cc_final: 0.7674 (ptt-90) REVERT: I 21 ASP cc_start: 0.7889 (t0) cc_final: 0.7181 (t0) REVERT: I 23 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8164 (mm-30) REVERT: I 230 LYS cc_start: 0.8361 (mmtp) cc_final: 0.8095 (mmtt) REVERT: I 271 GLU cc_start: 0.7914 (tp30) cc_final: 0.7655 (tt0) REVERT: J 244 GLU cc_start: 0.8114 (tt0) cc_final: 0.7676 (tp30) REVERT: K 6 LYS cc_start: 0.8300 (mttp) cc_final: 0.7831 (mttm) REVERT: K 21 ASP cc_start: 0.8240 (t0) cc_final: 0.7692 (t0) REVERT: K 76 ASN cc_start: 0.8621 (m110) cc_final: 0.7983 (m110) REVERT: K 90 ARG cc_start: 0.7185 (mmt90) cc_final: 0.6160 (mmp-170) REVERT: K 123 ARG cc_start: 0.7514 (ptp-170) cc_final: 0.7038 (ptp90) REVERT: K 317 TYR cc_start: 0.8063 (m-80) cc_final: 0.7763 (m-80) REVERT: L 123 ARG cc_start: 0.6077 (ptt180) cc_final: 0.5711 (ptp90) REVERT: L 143 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7707 (mt-10) REVERT: L 148 ASP cc_start: 0.8133 (m-30) cc_final: 0.7906 (m-30) REVERT: L 169 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7723 (mm-40) REVERT: L 218 GLN cc_start: 0.8446 (mp10) cc_final: 0.7829 (mp10) REVERT: L 272 GLU cc_start: 0.7150 (tt0) cc_final: 0.6889 (mm-30) REVERT: L 304 ARG cc_start: 0.8611 (mtt180) cc_final: 0.7064 (ttt180) REVERT: L 309 ARG cc_start: 0.6561 (mtm180) cc_final: 0.6187 (mtt90) outliers start: 84 outliers final: 61 residues processed: 528 average time/residue: 0.4273 time to fit residues: 350.2482 Evaluate side-chains 526 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 459 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 279 ILE Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 321 optimal weight: 30.0000 chunk 166 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 267 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 358 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 354 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN F 73 ASN F 76 ASN I 71 GLN I 76 ASN J 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.120864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.091683 restraints weight = 36764.719| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.58 r_work: 0.2777 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 29544 Z= 0.258 Angle : 0.664 9.511 40236 Z= 0.340 Chirality : 0.047 0.189 4428 Planarity : 0.005 0.062 5268 Dihedral : 5.516 28.423 4129 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.57 % Favored : 97.11 % Rotamer: Outliers : 3.01 % Allowed : 12.55 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.06 (0.14), residues: 3768 helix: -0.64 (0.14), residues: 1308 sheet: -1.39 (0.17), residues: 888 loop : -0.03 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 50 HIS 0.005 0.002 HIS I 167 PHE 0.014 0.002 PHE J 103 TYR 0.013 0.002 TYR E 297 ARG 0.005 0.001 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 1169) hydrogen bonds : angle 5.54079 ( 3282) covalent geometry : bond 0.00610 (29544) covalent geometry : angle 0.66374 (40236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 456 time to evaluate : 3.044 Fit side-chains REVERT: A 143 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7118 (mt-10) REVERT: A 148 ASP cc_start: 0.7747 (m-30) cc_final: 0.7376 (m-30) REVERT: A 169 GLN cc_start: 0.6417 (mp10) cc_final: 0.5422 (mp10) REVERT: A 301 ASP cc_start: 0.7334 (m-30) cc_final: 0.6988 (p0) REVERT: A 312 MET cc_start: 0.7383 (mtt) cc_final: 0.7111 (mtt) REVERT: A 313 THR cc_start: 0.7608 (p) cc_final: 0.7172 (t) REVERT: B 86 GLU cc_start: 0.4950 (mm-30) cc_final: 0.4595 (tt0) REVERT: B 118 ILE cc_start: 0.7306 (mt) cc_final: 0.6986 (mm) REVERT: B 134 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7697 (p) REVERT: B 141 TYR cc_start: 0.8362 (m-80) cc_final: 0.7942 (m-80) REVERT: C 71 GLN cc_start: 0.8151 (tt0) cc_final: 0.7926 (tt0) REVERT: C 96 LYS cc_start: 0.6649 (tppt) cc_final: 0.6114 (tptt) REVERT: C 123 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6215 (ptp90) REVERT: C 254 MET cc_start: 0.8794 (mmp) cc_final: 0.8528 (mmt) REVERT: D 50 TRP cc_start: 0.8574 (t60) cc_final: 0.8194 (t60) REVERT: D 76 ASN cc_start: 0.8584 (m-40) cc_final: 0.7988 (m110) REVERT: D 90 ARG cc_start: 0.7175 (mmt90) cc_final: 0.6248 (mmp-170) REVERT: D 254 MET cc_start: 0.8835 (mmt) cc_final: 0.8603 (mmp) REVERT: D 310 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7930 (mm-30) REVERT: E 23 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7237 (mm-30) REVERT: E 71 GLN cc_start: 0.8367 (tt0) cc_final: 0.7983 (tt0) REVERT: E 123 ARG cc_start: 0.7427 (ptt-90) cc_final: 0.6940 (ptt-90) REVERT: E 297 TYR cc_start: 0.8956 (t80) cc_final: 0.8570 (t80) REVERT: E 312 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8109 (mtm) REVERT: F 6 LYS cc_start: 0.7991 (mttp) cc_final: 0.7275 (mtpt) REVERT: F 21 ASP cc_start: 0.7851 (t0) cc_final: 0.7172 (t0) REVERT: G 121 CYS cc_start: 0.8028 (m) cc_final: 0.7627 (t) REVERT: H 21 ASP cc_start: 0.8400 (t70) cc_final: 0.8094 (t70) REVERT: H 96 LYS cc_start: 0.7598 (mmtt) cc_final: 0.6779 (mptt) REVERT: H 123 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7649 (ptt-90) REVERT: I 21 ASP cc_start: 0.8012 (t0) cc_final: 0.7312 (t70) REVERT: I 23 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8254 (mm-30) REVERT: I 271 GLU cc_start: 0.7969 (tp30) cc_final: 0.7717 (tt0) REVERT: J 76 ASN cc_start: 0.8775 (m-40) cc_final: 0.8371 (m110) REVERT: J 244 GLU cc_start: 0.8084 (tt0) cc_final: 0.7660 (tp30) REVERT: K 6 LYS cc_start: 0.8297 (mttp) cc_final: 0.7838 (mttm) REVERT: K 76 ASN cc_start: 0.8636 (m110) cc_final: 0.8000 (m110) REVERT: K 90 ARG cc_start: 0.7417 (mmt90) cc_final: 0.6377 (mmp-170) REVERT: K 123 ARG cc_start: 0.7388 (ptp-170) cc_final: 0.6912 (ptp90) REVERT: K 317 TYR cc_start: 0.8041 (m-80) cc_final: 0.7704 (m-80) REVERT: L 123 ARG cc_start: 0.6053 (ptt180) cc_final: 0.5701 (ptp90) REVERT: L 169 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7707 (mm-40) REVERT: L 218 GLN cc_start: 0.8485 (mp10) cc_final: 0.7871 (mp10) REVERT: L 304 ARG cc_start: 0.8657 (mtt180) cc_final: 0.7060 (ttt180) REVERT: L 309 ARG cc_start: 0.6588 (mtm180) cc_final: 0.5910 (mtm180) outliers start: 87 outliers final: 65 residues processed: 502 average time/residue: 0.4233 time to fit residues: 331.5822 Evaluate side-chains 507 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 438 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 123 ARG Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 279 ILE Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 345 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 316 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 258 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 365 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN F 73 ASN I 71 GLN I 76 ASN K 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.123610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.095457 restraints weight = 36679.623| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.49 r_work: 0.2829 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29544 Z= 0.140 Angle : 0.567 9.810 40236 Z= 0.293 Chirality : 0.043 0.175 4428 Planarity : 0.004 0.042 5268 Dihedral : 5.028 27.205 4129 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.23 % Favored : 97.45 % Rotamer: Outliers : 2.42 % Allowed : 13.42 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3768 helix: -0.34 (0.15), residues: 1308 sheet: -1.36 (0.17), residues: 840 loop : 0.04 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 59 HIS 0.005 0.001 HIS G 167 PHE 0.010 0.001 PHE F 69 TYR 0.009 0.001 TYR E 297 ARG 0.003 0.000 ARG G 106 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 1169) hydrogen bonds : angle 5.15948 ( 3282) covalent geometry : bond 0.00327 (29544) covalent geometry : angle 0.56731 (40236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 493 time to evaluate : 3.056 Fit side-chains REVERT: A 98 TYR cc_start: 0.7439 (m-80) cc_final: 0.7082 (m-80) REVERT: A 143 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6820 (mt-10) REVERT: A 148 ASP cc_start: 0.7663 (m-30) cc_final: 0.7244 (m-30) REVERT: A 169 GLN cc_start: 0.6429 (mp10) cc_final: 0.5543 (mp10) REVERT: A 185 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7727 (mp) REVERT: A 301 ASP cc_start: 0.7354 (m-30) cc_final: 0.6919 (p0) REVERT: A 312 MET cc_start: 0.7313 (mtt) cc_final: 0.7037 (mtt) REVERT: A 313 THR cc_start: 0.7555 (p) cc_final: 0.7149 (t) REVERT: B 86 GLU cc_start: 0.5001 (mm-30) cc_final: 0.4622 (tt0) REVERT: B 106 ARG cc_start: 0.6969 (ptt-90) cc_final: 0.5908 (ptt-90) REVERT: B 118 ILE cc_start: 0.7228 (mt) cc_final: 0.6902 (mm) REVERT: B 134 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7687 (p) REVERT: B 141 TYR cc_start: 0.8346 (m-80) cc_final: 0.7856 (m-80) REVERT: B 143 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7388 (mt-10) REVERT: C 39 GLU cc_start: 0.7810 (tp30) cc_final: 0.7520 (mm-30) REVERT: C 96 LYS cc_start: 0.6613 (tppt) cc_final: 0.6069 (tptt) REVERT: C 123 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6270 (ptp90) REVERT: C 254 MET cc_start: 0.8705 (mmp) cc_final: 0.8366 (mmt) REVERT: D 50 TRP cc_start: 0.8501 (t60) cc_final: 0.8067 (t60) REVERT: D 76 ASN cc_start: 0.8475 (m-40) cc_final: 0.7770 (m110) REVERT: D 90 ARG cc_start: 0.7097 (mmt90) cc_final: 0.6147 (mmp-170) REVERT: D 254 MET cc_start: 0.8738 (mmt) cc_final: 0.8491 (mmp) REVERT: D 310 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7892 (mm-30) REVERT: E 23 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7286 (mm-30) REVERT: E 39 GLU cc_start: 0.8241 (tp30) cc_final: 0.7971 (tp30) REVERT: E 90 ARG cc_start: 0.6370 (mmp-170) cc_final: 0.5278 (mtm110) REVERT: E 123 ARG cc_start: 0.7486 (ptt-90) cc_final: 0.7133 (ptt-90) REVERT: E 271 GLU cc_start: 0.8131 (tp30) cc_final: 0.7893 (mm-30) REVERT: E 312 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.8009 (mtm) REVERT: F 6 LYS cc_start: 0.7975 (mttp) cc_final: 0.7364 (mtpt) REVERT: F 21 ASP cc_start: 0.7833 (t0) cc_final: 0.7312 (t0) REVERT: G 23 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8036 (mm-30) REVERT: G 121 CYS cc_start: 0.7682 (m) cc_final: 0.7405 (t) REVERT: G 206 ASN cc_start: 0.8755 (m-40) cc_final: 0.8266 (m-40) REVERT: H 21 ASP cc_start: 0.8410 (t70) cc_final: 0.8103 (t70) REVERT: H 96 LYS cc_start: 0.7585 (mmtt) cc_final: 0.6882 (mptt) REVERT: H 123 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7575 (ptt-90) REVERT: H 206 ASN cc_start: 0.8749 (m-40) cc_final: 0.8267 (m-40) REVERT: I 21 ASP cc_start: 0.7903 (t0) cc_final: 0.7202 (t0) REVERT: I 23 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8279 (mm-30) REVERT: I 271 GLU cc_start: 0.7953 (tp30) cc_final: 0.7690 (tt0) REVERT: J 94 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7439 (mt0) REVERT: J 244 GLU cc_start: 0.8164 (tt0) cc_final: 0.7817 (tp30) REVERT: K 6 LYS cc_start: 0.8286 (mttp) cc_final: 0.7811 (mttm) REVERT: K 21 ASP cc_start: 0.8211 (t0) cc_final: 0.7717 (t0) REVERT: K 90 ARG cc_start: 0.7130 (mmt90) cc_final: 0.6154 (mmp-170) REVERT: K 123 ARG cc_start: 0.7442 (ptp-170) cc_final: 0.7045 (ptp90) REVERT: L 123 ARG cc_start: 0.6153 (ptt180) cc_final: 0.5789 (ptp90) REVERT: L 143 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7551 (mt-10) REVERT: L 169 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7717 (mm-40) REVERT: L 218 GLN cc_start: 0.8372 (mp10) cc_final: 0.7792 (mp10) REVERT: L 254 MET cc_start: 0.8468 (mmp) cc_final: 0.8161 (tpt) REVERT: L 304 ARG cc_start: 0.8587 (mtt180) cc_final: 0.7020 (ttt180) REVERT: L 309 ARG cc_start: 0.6513 (mtm180) cc_final: 0.6211 (mtt90) REVERT: L 314 ARG cc_start: 0.8310 (mpt90) cc_final: 0.8103 (mpt90) outliers start: 70 outliers final: 46 residues processed: 530 average time/residue: 0.4161 time to fit residues: 344.5565 Evaluate side-chains 519 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 468 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 123 ARG Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 279 ILE Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 166 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 276 optimal weight: 1.9990 chunk 181 optimal weight: 30.0000 chunk 155 optimal weight: 20.0000 chunk 106 optimal weight: 0.7980 chunk 92 optimal weight: 0.0050 chunk 158 optimal weight: 8.9990 chunk 369 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 356 optimal weight: 30.0000 overall best weight: 6.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN F 76 ASN H 169 GLN I 71 GLN I 76 ASN J 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.121370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.092965 restraints weight = 37045.459| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.49 r_work: 0.2783 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29544 Z= 0.216 Angle : 0.631 10.092 40236 Z= 0.323 Chirality : 0.046 0.177 4428 Planarity : 0.004 0.050 5268 Dihedral : 5.265 27.433 4129 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.23 % Favored : 97.45 % Rotamer: Outliers : 2.66 % Allowed : 13.76 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3768 helix: -0.43 (0.15), residues: 1308 sheet: -1.43 (0.16), residues: 924 loop : 0.14 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 50 HIS 0.004 0.001 HIS H 180 PHE 0.011 0.002 PHE I 69 TYR 0.011 0.001 TYR I 297 ARG 0.004 0.001 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 1169) hydrogen bonds : angle 5.37018 ( 3282) covalent geometry : bond 0.00513 (29544) covalent geometry : angle 0.63067 (40236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 456 time to evaluate : 2.900 Fit side-chains REVERT: A 143 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6973 (mt-10) REVERT: A 148 ASP cc_start: 0.7736 (m-30) cc_final: 0.7275 (m-30) REVERT: A 169 GLN cc_start: 0.6396 (mp10) cc_final: 0.5450 (mp10) REVERT: A 185 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7824 (mp) REVERT: A 248 GLU cc_start: 0.6675 (tp30) cc_final: 0.6369 (tp30) REVERT: A 301 ASP cc_start: 0.7290 (m-30) cc_final: 0.6883 (p0) REVERT: A 312 MET cc_start: 0.7350 (mtt) cc_final: 0.7101 (mtt) REVERT: A 313 THR cc_start: 0.7548 (p) cc_final: 0.7165 (t) REVERT: B 86 GLU cc_start: 0.5007 (mm-30) cc_final: 0.4647 (tt0) REVERT: B 118 ILE cc_start: 0.7267 (mt) cc_final: 0.6969 (mm) REVERT: B 134 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7792 (p) REVERT: B 141 TYR cc_start: 0.8379 (m-80) cc_final: 0.7917 (m-80) REVERT: B 143 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7500 (mt-10) REVERT: B 279 ILE cc_start: 0.8246 (mm) cc_final: 0.7852 (mt) REVERT: C 96 LYS cc_start: 0.6689 (tppt) cc_final: 0.6108 (tptt) REVERT: C 123 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6281 (ptp90) REVERT: C 254 MET cc_start: 0.8750 (mmp) cc_final: 0.8499 (mmt) REVERT: D 50 TRP cc_start: 0.8518 (t60) cc_final: 0.8076 (t60) REVERT: D 76 ASN cc_start: 0.8537 (m-40) cc_final: 0.7915 (m110) REVERT: D 90 ARG cc_start: 0.7199 (mmt90) cc_final: 0.6196 (mmp-170) REVERT: D 254 MET cc_start: 0.8825 (mmt) cc_final: 0.8602 (mmp) REVERT: D 310 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7911 (mm-30) REVERT: E 23 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7260 (mm-30) REVERT: E 39 GLU cc_start: 0.8253 (tp30) cc_final: 0.7957 (tp30) REVERT: E 123 ARG cc_start: 0.7499 (ptt-90) cc_final: 0.7029 (ptt-90) REVERT: E 271 GLU cc_start: 0.8177 (tp30) cc_final: 0.7933 (mm-30) REVERT: F 6 LYS cc_start: 0.7960 (mttp) cc_final: 0.7358 (mtpt) REVERT: F 21 ASP cc_start: 0.7924 (t0) cc_final: 0.7329 (t0) REVERT: G 121 CYS cc_start: 0.7893 (m) cc_final: 0.7616 (t) REVERT: G 206 ASN cc_start: 0.8841 (m-40) cc_final: 0.8385 (m-40) REVERT: H 21 ASP cc_start: 0.8457 (t70) cc_final: 0.8126 (t70) REVERT: H 96 LYS cc_start: 0.7665 (mmtt) cc_final: 0.6929 (mptt) REVERT: H 123 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7677 (ptt-90) REVERT: H 206 ASN cc_start: 0.8835 (m-40) cc_final: 0.8378 (m-40) REVERT: I 21 ASP cc_start: 0.7926 (t0) cc_final: 0.7141 (t0) REVERT: I 23 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8275 (mm-30) REVERT: I 271 GLU cc_start: 0.7878 (tp30) cc_final: 0.7629 (tt0) REVERT: J 94 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7445 (mt0) REVERT: J 244 GLU cc_start: 0.8206 (tt0) cc_final: 0.7865 (tp30) REVERT: K 6 LYS cc_start: 0.8266 (mttp) cc_final: 0.7793 (mttm) REVERT: K 76 ASN cc_start: 0.8644 (m110) cc_final: 0.8150 (m110) REVERT: K 90 ARG cc_start: 0.7278 (mmt90) cc_final: 0.6201 (mmp-170) REVERT: K 123 ARG cc_start: 0.7507 (ptp-170) cc_final: 0.7178 (ptp90) REVERT: L 123 ARG cc_start: 0.6179 (ptt180) cc_final: 0.5805 (ptp90) REVERT: L 143 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7707 (mt-10) REVERT: L 148 ASP cc_start: 0.8108 (m-30) cc_final: 0.7890 (m-30) REVERT: L 169 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7701 (mm-40) REVERT: L 218 GLN cc_start: 0.8407 (mp10) cc_final: 0.7831 (mp10) REVERT: L 304 ARG cc_start: 0.8627 (mtt180) cc_final: 0.7054 (ttt180) REVERT: L 309 ARG cc_start: 0.6555 (mtm180) cc_final: 0.6262 (mtt90) outliers start: 77 outliers final: 61 residues processed: 496 average time/residue: 0.4219 time to fit residues: 327.7454 Evaluate side-chains 512 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 447 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 231 GLU Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 123 ARG Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 312 MET Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 346 optimal weight: 7.9990 chunk 41 optimal weight: 30.0000 chunk 183 optimal weight: 7.9990 chunk 214 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 270 optimal weight: 0.0670 chunk 337 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 overall best weight: 3.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN F 76 ASN I 71 GLN I 76 ASN J 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.123545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.095315 restraints weight = 36833.394| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.50 r_work: 0.2822 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29544 Z= 0.149 Angle : 0.579 9.820 40236 Z= 0.297 Chirality : 0.044 0.165 4428 Planarity : 0.004 0.042 5268 Dihedral : 5.010 26.869 4129 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.26 % Favored : 97.43 % Rotamer: Outliers : 2.56 % Allowed : 14.11 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3768 helix: -0.27 (0.15), residues: 1308 sheet: -1.35 (0.18), residues: 816 loop : 0.12 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 59 HIS 0.004 0.001 HIS F 152 PHE 0.009 0.001 PHE F 69 TYR 0.008 0.001 TYR I 297 ARG 0.003 0.000 ARG G 106 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 1169) hydrogen bonds : angle 5.15657 ( 3282) covalent geometry : bond 0.00352 (29544) covalent geometry : angle 0.57938 (40236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 473 time to evaluate : 2.893 Fit side-chains REVERT: A 143 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6878 (mt-10) REVERT: A 148 ASP cc_start: 0.7701 (m-30) cc_final: 0.7207 (m-30) REVERT: A 169 GLN cc_start: 0.6481 (mp10) cc_final: 0.5559 (mp10) REVERT: A 185 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7786 (mp) REVERT: A 248 GLU cc_start: 0.6731 (tp30) cc_final: 0.6427 (tp30) REVERT: A 301 ASP cc_start: 0.7275 (m-30) cc_final: 0.6879 (p0) REVERT: A 312 MET cc_start: 0.7297 (mtt) cc_final: 0.7028 (mtt) REVERT: A 313 THR cc_start: 0.7564 (p) cc_final: 0.7191 (t) REVERT: B 86 GLU cc_start: 0.4991 (mm-30) cc_final: 0.4597 (tt0) REVERT: B 106 ARG cc_start: 0.6999 (ptt-90) cc_final: 0.5924 (ptt-90) REVERT: B 118 ILE cc_start: 0.7158 (mt) cc_final: 0.6783 (mm) REVERT: B 134 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7697 (p) REVERT: B 141 TYR cc_start: 0.8385 (m-80) cc_final: 0.7877 (m-80) REVERT: B 143 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7291 (mt-10) REVERT: B 216 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7889 (mt-10) REVERT: C 96 LYS cc_start: 0.6666 (tppt) cc_final: 0.6070 (tptt) REVERT: C 123 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.6353 (ptp90) REVERT: C 254 MET cc_start: 0.8617 (mmp) cc_final: 0.8260 (mmt) REVERT: D 76 ASN cc_start: 0.8481 (m-40) cc_final: 0.7823 (m110) REVERT: D 90 ARG cc_start: 0.7175 (mmt90) cc_final: 0.6125 (mmp-170) REVERT: D 254 MET cc_start: 0.8767 (mmt) cc_final: 0.8535 (mmp) REVERT: D 310 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7839 (mm-30) REVERT: E 39 GLU cc_start: 0.8269 (tp30) cc_final: 0.7902 (tp30) REVERT: E 123 ARG cc_start: 0.7493 (ptt-90) cc_final: 0.7051 (ptt-90) REVERT: E 271 GLU cc_start: 0.8133 (tp30) cc_final: 0.7889 (mm-30) REVERT: F 6 LYS cc_start: 0.7971 (mttp) cc_final: 0.7362 (mtpt) REVERT: F 21 ASP cc_start: 0.7911 (t0) cc_final: 0.7347 (t0) REVERT: G 23 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8024 (mm-30) REVERT: G 121 CYS cc_start: 0.7760 (m) cc_final: 0.7439 (t) REVERT: G 206 ASN cc_start: 0.8759 (m-40) cc_final: 0.8248 (m-40) REVERT: H 21 ASP cc_start: 0.8395 (t70) cc_final: 0.7933 (t70) REVERT: H 96 LYS cc_start: 0.7696 (mmtt) cc_final: 0.6955 (mptt) REVERT: H 123 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7719 (ptt-90) REVERT: H 206 ASN cc_start: 0.8781 (m-40) cc_final: 0.8296 (m-40) REVERT: I 21 ASP cc_start: 0.7937 (t0) cc_final: 0.7266 (t0) REVERT: I 23 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8281 (mm-30) REVERT: I 271 GLU cc_start: 0.7932 (tp30) cc_final: 0.7693 (tt0) REVERT: J 94 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7460 (mt0) REVERT: J 244 GLU cc_start: 0.8188 (tt0) cc_final: 0.7771 (tp30) REVERT: J 312 MET cc_start: 0.8281 (mtm) cc_final: 0.8006 (mtm) REVERT: K 6 LYS cc_start: 0.8270 (mttp) cc_final: 0.7791 (mttm) REVERT: K 76 ASN cc_start: 0.8616 (m110) cc_final: 0.8119 (m110) REVERT: K 90 ARG cc_start: 0.7257 (mmt90) cc_final: 0.6134 (mmp-170) REVERT: K 123 ARG cc_start: 0.7392 (ptp-170) cc_final: 0.7019 (ptp90) REVERT: L 21 ASP cc_start: 0.6906 (t0) cc_final: 0.6310 (m-30) REVERT: L 96 LYS cc_start: 0.6594 (mmtt) cc_final: 0.6364 (mmtt) REVERT: L 123 ARG cc_start: 0.6147 (ptt180) cc_final: 0.5786 (ptp90) REVERT: L 143 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7590 (mt-10) REVERT: L 169 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7712 (mm-40) REVERT: L 218 GLN cc_start: 0.8378 (mp10) cc_final: 0.7812 (mp10) REVERT: L 254 MET cc_start: 0.8425 (mmp) cc_final: 0.8164 (tpt) REVERT: L 304 ARG cc_start: 0.8594 (mtt180) cc_final: 0.7040 (ttt180) REVERT: L 309 ARG cc_start: 0.6558 (mtm180) cc_final: 0.6310 (mtt90) outliers start: 74 outliers final: 58 residues processed: 509 average time/residue: 0.4240 time to fit residues: 337.0087 Evaluate side-chains 523 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 461 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 123 ARG Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 279 ILE Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 312 MET Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2466 > 50: distance: 122 - 127: 23.892 distance: 123 - 146: 36.598 distance: 127 - 128: 17.827 distance: 128 - 129: 26.634 distance: 128 - 131: 51.932 distance: 129 - 130: 20.806 distance: 129 - 135: 21.533 distance: 130 - 151: 40.713 distance: 131 - 132: 32.947 distance: 131 - 133: 42.138 distance: 132 - 134: 39.321 distance: 135 - 136: 56.072 distance: 136 - 137: 18.251 distance: 137 - 138: 40.899 distance: 137 - 139: 38.954 distance: 139 - 140: 17.989 distance: 140 - 141: 18.484 distance: 140 - 143: 46.083 distance: 141 - 142: 40.012 distance: 141 - 146: 36.351 distance: 143 - 144: 38.817 distance: 143 - 145: 32.658 distance: 146 - 147: 69.825 distance: 147 - 148: 41.971 distance: 147 - 150: 57.553 distance: 148 - 149: 48.668 distance: 148 - 151: 42.053 distance: 152 - 153: 26.941 distance: 152 - 155: 61.700 distance: 153 - 154: 41.231 distance: 153 - 160: 14.775 distance: 155 - 156: 22.241 distance: 156 - 157: 43.118 distance: 157 - 158: 25.347 distance: 158 - 159: 45.462 distance: 160 - 161: 51.139 distance: 161 - 162: 32.743 distance: 161 - 164: 30.624 distance: 162 - 163: 39.467 distance: 162 - 165: 55.636 distance: 165 - 166: 51.123 distance: 166 - 167: 11.160 distance: 166 - 169: 40.380 distance: 167 - 168: 27.439 distance: 167 - 170: 42.726 distance: 170 - 171: 22.246 distance: 171 - 172: 42.603 distance: 171 - 174: 60.035 distance: 172 - 173: 39.356 distance: 174 - 175: 39.930 distance: 175 - 176: 47.714 distance: 175 - 177: 41.134 distance: 176 - 178: 56.637 distance: 177 - 179: 46.066 distance: 178 - 180: 27.051 distance: 179 - 180: 42.324 distance: 180 - 181: 12.977 distance: 182 - 183: 50.952 distance: 183 - 184: 40.757 distance: 183 - 186: 5.337 distance: 184 - 185: 51.846 distance: 184 - 190: 58.196 distance: 186 - 187: 43.322 distance: 187 - 188: 34.668 distance: 187 - 189: 53.636 distance: 190 - 191: 48.491 distance: 190 - 196: 46.785 distance: 191 - 192: 16.229 distance: 191 - 194: 22.509 distance: 192 - 193: 63.506 distance: 192 - 197: 34.668 distance: 194 - 195: 39.979 distance: 195 - 196: 29.642