Starting phenix.real_space_refine on Tue Aug 26 03:07:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j0c_9761/08_2025/6j0c_9761.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j0c_9761/08_2025/6j0c_9761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6j0c_9761/08_2025/6j0c_9761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j0c_9761/08_2025/6j0c_9761.map" model { file = "/net/cci-nas-00/data/ceres_data/6j0c_9761/08_2025/6j0c_9761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j0c_9761/08_2025/6j0c_9761.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.025 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 108 5.16 5 C 21120 2.51 5 N 5484 2.21 5 O 6396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 360 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33108 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: B, C, D, E, F, a, b, c, d, e, f Time building chain proxies: 3.72, per 1000 atoms: 0.11 Number of scatterers: 33108 At special positions: 0 Unit cell: (232.047, 233.168, 78.47, 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 108 16.00 O 6396 8.00 N 5484 7.00 C 21120 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7896 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 66 sheets defined 31.6% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.580A pdb=" N ILE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.825A pdb=" N VAL A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 removed outlier: 4.046A pdb=" N PHE A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 66 through 79 removed outlier: 3.525A pdb=" N ARG B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.580A pdb=" N ILE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 171 through 187 removed outlier: 3.826A pdb=" N VAL B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 267 removed outlier: 4.046A pdb=" N PHE B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 284 " --> pdb=" O TRP B 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 Processing helix chain 'C' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 111 through 119 Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 171 through 187 removed outlier: 3.826A pdb=" N VAL C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 179 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 267 removed outlier: 4.046A pdb=" N PHE C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 Processing helix chain 'D' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG D 73 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 90 through 95' Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 171 through 187 removed outlier: 3.825A pdb=" N VAL D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 179 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 267 removed outlier: 4.046A pdb=" N PHE D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU D 260 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 284 " --> pdb=" O TRP D 280 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 56 Processing helix chain 'E' and resid 66 through 79 removed outlier: 3.525A pdb=" N ARG E 73 " --> pdb=" O ASP E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 95 removed outlier: 3.580A pdb=" N ILE E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 90 through 95' Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 171 through 187 removed outlier: 3.826A pdb=" N VAL E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL E 179 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG E 282 " --> pdb=" O PRO E 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG E 284 " --> pdb=" O TRP E 280 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 308 Processing helix chain 'E' and resid 320 through 326 removed outlier: 3.602A pdb=" N ILE E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 56 Processing helix chain 'F' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE F 94 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 90 through 95' Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 111 through 119 Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 171 through 187 removed outlier: 3.826A pdb=" N VAL F 175 " --> pdb=" O PRO F 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL F 179 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA F 181 " --> pdb=" O ALA F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU F 260 " --> pdb=" O PHE F 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS F 264 " --> pdb=" O GLU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 297 removed outlier: 3.826A pdb=" N ARG F 282 " --> pdb=" O PRO F 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 284 " --> pdb=" O TRP F 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR F 290 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 56 Processing helix chain 'a' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG a 73 " --> pdb=" O ASP a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE a 94 " --> pdb=" O SER a 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE a 95 " --> pdb=" O LEU a 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 90 through 95' Processing helix chain 'a' and resid 96 through 98 No H-bonds generated for 'chain 'a' and resid 96 through 98' Processing helix chain 'a' and resid 111 through 119 Processing helix chain 'a' and resid 140 through 145 Processing helix chain 'a' and resid 171 through 187 removed outlier: 3.826A pdb=" N VAL a 175 " --> pdb=" O PRO a 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY a 178 " --> pdb=" O ALA a 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL a 179 " --> pdb=" O VAL a 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA a 181 " --> pdb=" O ALA a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE a 256 " --> pdb=" O VAL a 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU a 260 " --> pdb=" O PHE a 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS a 264 " --> pdb=" O GLU a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 278 through 297 removed outlier: 3.826A pdb=" N ARG a 282 " --> pdb=" O PRO a 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG a 284 " --> pdb=" O TRP a 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR a 290 " --> pdb=" O ALA a 286 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP a 295 " --> pdb=" O LEU a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 304 through 308 Processing helix chain 'a' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE a 324 " --> pdb=" O THR a 320 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 56 Processing helix chain 'b' and resid 66 through 79 removed outlier: 3.525A pdb=" N ARG b 73 " --> pdb=" O ASP b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 90 through 95 removed outlier: 3.580A pdb=" N ILE b 94 " --> pdb=" O SER b 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE b 95 " --> pdb=" O LEU b 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 90 through 95' Processing helix chain 'b' and resid 96 through 98 No H-bonds generated for 'chain 'b' and resid 96 through 98' Processing helix chain 'b' and resid 111 through 119 Processing helix chain 'b' and resid 140 through 145 Processing helix chain 'b' and resid 171 through 187 removed outlier: 3.827A pdb=" N VAL b 175 " --> pdb=" O PRO b 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY b 178 " --> pdb=" O ALA b 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL b 179 " --> pdb=" O VAL b 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA b 181 " --> pdb=" O ALA b 177 " (cutoff:3.500A) Processing helix chain 'b' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE b 256 " --> pdb=" O VAL b 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU b 260 " --> pdb=" O PHE b 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS b 264 " --> pdb=" O GLU b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG b 282 " --> pdb=" O PRO b 278 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG b 284 " --> pdb=" O TRP b 280 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR b 290 " --> pdb=" O ALA b 286 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP b 295 " --> pdb=" O LEU b 291 " (cutoff:3.500A) Processing helix chain 'b' and resid 304 through 308 Processing helix chain 'b' and resid 320 through 326 removed outlier: 3.604A pdb=" N ILE b 324 " --> pdb=" O THR b 320 " (cutoff:3.500A) Processing helix chain 'c' and resid 51 through 56 Processing helix chain 'c' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG c 73 " --> pdb=" O ASP c 69 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE c 94 " --> pdb=" O SER c 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE c 95 " --> pdb=" O LEU c 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 90 through 95' Processing helix chain 'c' and resid 96 through 98 No H-bonds generated for 'chain 'c' and resid 96 through 98' Processing helix chain 'c' and resid 111 through 119 Processing helix chain 'c' and resid 140 through 145 Processing helix chain 'c' and resid 171 through 187 removed outlier: 3.825A pdb=" N VAL c 175 " --> pdb=" O PRO c 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY c 178 " --> pdb=" O ALA c 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL c 179 " --> pdb=" O VAL c 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA c 181 " --> pdb=" O ALA c 177 " (cutoff:3.500A) Processing helix chain 'c' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE c 256 " --> pdb=" O VAL c 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU c 260 " --> pdb=" O PHE c 256 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS c 264 " --> pdb=" O GLU c 260 " (cutoff:3.500A) Processing helix chain 'c' and resid 278 through 297 removed outlier: 3.826A pdb=" N ARG c 282 " --> pdb=" O PRO c 278 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG c 284 " --> pdb=" O TRP c 280 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR c 290 " --> pdb=" O ALA c 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP c 295 " --> pdb=" O LEU c 291 " (cutoff:3.500A) Processing helix chain 'c' and resid 304 through 308 Processing helix chain 'c' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE c 324 " --> pdb=" O THR c 320 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 56 Processing helix chain 'd' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG d 73 " --> pdb=" O ASP d 69 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE d 94 " --> pdb=" O SER d 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE d 95 " --> pdb=" O LEU d 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 90 through 95' Processing helix chain 'd' and resid 96 through 98 No H-bonds generated for 'chain 'd' and resid 96 through 98' Processing helix chain 'd' and resid 111 through 119 Processing helix chain 'd' and resid 140 through 145 Processing helix chain 'd' and resid 171 through 187 removed outlier: 3.825A pdb=" N VAL d 175 " --> pdb=" O PRO d 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY d 178 " --> pdb=" O ALA d 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL d 179 " --> pdb=" O VAL d 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA d 181 " --> pdb=" O ALA d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE d 256 " --> pdb=" O VAL d 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU d 260 " --> pdb=" O PHE d 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS d 264 " --> pdb=" O GLU d 260 " (cutoff:3.500A) Processing helix chain 'd' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG d 282 " --> pdb=" O PRO d 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG d 284 " --> pdb=" O TRP d 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR d 290 " --> pdb=" O ALA d 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP d 295 " --> pdb=" O LEU d 291 " (cutoff:3.500A) Processing helix chain 'd' and resid 304 through 308 Processing helix chain 'd' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE d 324 " --> pdb=" O THR d 320 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 56 Processing helix chain 'e' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG e 73 " --> pdb=" O ASP e 69 " (cutoff:3.500A) Processing helix chain 'e' and resid 90 through 95 removed outlier: 3.580A pdb=" N ILE e 94 " --> pdb=" O SER e 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE e 95 " --> pdb=" O LEU e 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 90 through 95' Processing helix chain 'e' and resid 96 through 98 No H-bonds generated for 'chain 'e' and resid 96 through 98' Processing helix chain 'e' and resid 111 through 119 Processing helix chain 'e' and resid 140 through 145 Processing helix chain 'e' and resid 171 through 187 removed outlier: 3.825A pdb=" N VAL e 175 " --> pdb=" O PRO e 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY e 178 " --> pdb=" O ALA e 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL e 179 " --> pdb=" O VAL e 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA e 181 " --> pdb=" O ALA e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE e 256 " --> pdb=" O VAL e 252 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU e 260 " --> pdb=" O PHE e 256 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS e 264 " --> pdb=" O GLU e 260 " (cutoff:3.500A) Processing helix chain 'e' and resid 278 through 297 removed outlier: 3.824A pdb=" N ARG e 282 " --> pdb=" O PRO e 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG e 284 " --> pdb=" O TRP e 280 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR e 290 " --> pdb=" O ALA e 286 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP e 295 " --> pdb=" O LEU e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 304 through 308 Processing helix chain 'e' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE e 324 " --> pdb=" O THR e 320 " (cutoff:3.500A) Processing helix chain 'f' and resid 51 through 56 Processing helix chain 'f' and resid 66 through 79 removed outlier: 3.525A pdb=" N ARG f 73 " --> pdb=" O ASP f 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE f 94 " --> pdb=" O SER f 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE f 95 " --> pdb=" O LEU f 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 90 through 95' Processing helix chain 'f' and resid 96 through 98 No H-bonds generated for 'chain 'f' and resid 96 through 98' Processing helix chain 'f' and resid 111 through 119 Processing helix chain 'f' and resid 140 through 145 Processing helix chain 'f' and resid 171 through 187 removed outlier: 3.826A pdb=" N VAL f 175 " --> pdb=" O PRO f 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY f 178 " --> pdb=" O ALA f 174 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL f 179 " --> pdb=" O VAL f 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA f 181 " --> pdb=" O ALA f 177 " (cutoff:3.500A) Processing helix chain 'f' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE f 256 " --> pdb=" O VAL f 252 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU f 260 " --> pdb=" O PHE f 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS f 264 " --> pdb=" O GLU f 260 " (cutoff:3.500A) Processing helix chain 'f' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG f 282 " --> pdb=" O PRO f 278 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG f 284 " --> pdb=" O TRP f 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR f 290 " --> pdb=" O ALA f 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP f 295 " --> pdb=" O LEU f 291 " (cutoff:3.500A) Processing helix chain 'f' and resid 304 through 308 Processing helix chain 'f' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE f 324 " --> pdb=" O THR f 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.315A pdb=" N GLY A 9 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU B 346 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR A 11 " --> pdb=" O LEU B 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA A 127 " --> pdb=" O ALA A 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 312 removed outlier: 3.671A pdb=" N PHE A 310 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 331 " --> pdb=" O GLN a 347 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR a 349 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 333 " --> pdb=" O THR a 349 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 347 Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.318A pdb=" N GLY B 9 " --> pdb=" O ILE C 344 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU C 346 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR B 11 " --> pdb=" O LEU C 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA B 127 " --> pdb=" O ALA B 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 162 Processing sheet with id=AB3, first strand: chain 'B' and resid 225 through 228 Processing sheet with id=AB4, first strand: chain 'B' and resid 309 through 312 removed outlier: 3.670A pdb=" N PHE B 310 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 331 " --> pdb=" O GLN b 347 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR b 349 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL B 333 " --> pdb=" O THR b 349 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY a 9 " --> pdb=" O ILE b 344 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU b 346 " --> pdb=" O GLY a 9 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR a 11 " --> pdb=" O LEU b 346 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N PHE b 348 " --> pdb=" O TYR a 11 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLU a 13 " --> pdb=" O PHE b 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.324A pdb=" N GLY C 9 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU D 346 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR C 11 " --> pdb=" O LEU D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 47 through 49 Processing sheet with id=AB7, first strand: chain 'C' and resid 127 through 128 removed outlier: 7.461A pdb=" N ALA C 127 " --> pdb=" O ALA C 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AB9, first strand: chain 'C' and resid 225 through 228 Processing sheet with id=AC1, first strand: chain 'C' and resid 309 through 312 removed outlier: 3.670A pdb=" N PHE C 310 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 332 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL C 331 " --> pdb=" O GLN c 347 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR c 349 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL C 333 " --> pdb=" O THR c 349 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY b 9 " --> pdb=" O ILE c 344 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU c 346 " --> pdb=" O GLY b 9 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR b 11 " --> pdb=" O LEU c 346 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE c 348 " --> pdb=" O TYR b 11 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU b 13 " --> pdb=" O PHE c 348 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.348A pdb=" N GLY D 9 " --> pdb=" O ILE E 344 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU E 346 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR D 11 " --> pdb=" O LEU E 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 47 through 49 Processing sheet with id=AC4, first strand: chain 'D' and resid 127 through 128 removed outlier: 7.461A pdb=" N ALA D 127 " --> pdb=" O ALA D 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 161 through 162 Processing sheet with id=AC6, first strand: chain 'D' and resid 225 through 228 Processing sheet with id=AC7, first strand: chain 'D' and resid 309 through 312 removed outlier: 3.671A pdb=" N PHE D 310 " --> pdb=" O GLY D 334 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL D 331 " --> pdb=" O GLN d 347 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N THR d 349 " --> pdb=" O VAL D 331 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL D 333 " --> pdb=" O THR d 349 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY c 9 " --> pdb=" O ILE d 344 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU d 346 " --> pdb=" O GLY c 9 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR c 11 " --> pdb=" O LEU d 346 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE d 348 " --> pdb=" O TYR c 11 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLU c 13 " --> pdb=" O PHE d 348 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.309A pdb=" N GLY E 9 " --> pdb=" O ILE F 344 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU F 346 " --> pdb=" O GLY E 9 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR E 11 " --> pdb=" O LEU F 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 47 through 49 Processing sheet with id=AD1, first strand: chain 'E' and resid 127 through 128 removed outlier: 7.461A pdb=" N ALA E 127 " --> pdb=" O ALA E 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 161 through 162 Processing sheet with id=AD3, first strand: chain 'E' and resid 225 through 228 Processing sheet with id=AD4, first strand: chain 'E' and resid 309 through 312 removed outlier: 3.671A pdb=" N PHE E 310 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL E 331 " --> pdb=" O GLN e 347 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR e 349 " --> pdb=" O VAL E 331 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL E 333 " --> pdb=" O THR e 349 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY d 9 " --> pdb=" O ILE e 344 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU e 346 " --> pdb=" O GLY d 9 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR d 11 " --> pdb=" O LEU e 346 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE e 348 " --> pdb=" O TYR d 11 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU d 13 " --> pdb=" O PHE e 348 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 47 through 49 Processing sheet with id=AD6, first strand: chain 'F' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA F 127 " --> pdb=" O ALA F 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'F' and resid 161 through 162 Processing sheet with id=AD8, first strand: chain 'F' and resid 225 through 228 Processing sheet with id=AD9, first strand: chain 'F' and resid 309 through 312 removed outlier: 3.670A pdb=" N PHE F 310 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL F 331 " --> pdb=" O GLN f 347 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR f 349 " --> pdb=" O VAL F 331 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL F 333 " --> pdb=" O THR f 349 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY e 9 " --> pdb=" O ILE f 344 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU f 346 " --> pdb=" O GLY e 9 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR e 11 " --> pdb=" O LEU f 346 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N PHE f 348 " --> pdb=" O TYR e 11 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLU e 13 " --> pdb=" O PHE f 348 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'a' and resid 47 through 49 Processing sheet with id=AE2, first strand: chain 'a' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA a 127 " --> pdb=" O ALA a 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'a' and resid 161 through 162 Processing sheet with id=AE4, first strand: chain 'a' and resid 225 through 228 Processing sheet with id=AE5, first strand: chain 'a' and resid 309 through 312 removed outlier: 3.670A pdb=" N PHE a 310 " --> pdb=" O GLY a 334 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'b' and resid 47 through 49 Processing sheet with id=AE7, first strand: chain 'b' and resid 127 through 128 removed outlier: 7.461A pdb=" N ALA b 127 " --> pdb=" O ALA b 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'b' and resid 161 through 162 Processing sheet with id=AE9, first strand: chain 'b' and resid 225 through 228 Processing sheet with id=AF1, first strand: chain 'b' and resid 309 through 312 removed outlier: 3.671A pdb=" N PHE b 310 " --> pdb=" O GLY b 334 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 47 through 49 Processing sheet with id=AF3, first strand: chain 'c' and resid 127 through 128 removed outlier: 7.461A pdb=" N ALA c 127 " --> pdb=" O ALA c 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'c' and resid 161 through 162 Processing sheet with id=AF5, first strand: chain 'c' and resid 225 through 228 Processing sheet with id=AF6, first strand: chain 'c' and resid 309 through 312 removed outlier: 3.671A pdb=" N PHE c 310 " --> pdb=" O GLY c 334 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'd' and resid 47 through 49 Processing sheet with id=AF8, first strand: chain 'd' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA d 127 " --> pdb=" O ALA d 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'd' and resid 161 through 162 Processing sheet with id=AG1, first strand: chain 'd' and resid 225 through 228 Processing sheet with id=AG2, first strand: chain 'd' and resid 309 through 312 removed outlier: 3.670A pdb=" N PHE d 310 " --> pdb=" O GLY d 334 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'e' and resid 47 through 49 Processing sheet with id=AG4, first strand: chain 'e' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA e 127 " --> pdb=" O ALA e 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'e' and resid 161 through 162 Processing sheet with id=AG6, first strand: chain 'e' and resid 225 through 228 Processing sheet with id=AG7, first strand: chain 'e' and resid 309 through 312 removed outlier: 3.670A pdb=" N PHE e 310 " --> pdb=" O GLY e 334 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'f' and resid 47 through 49 Processing sheet with id=AG9, first strand: chain 'f' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA f 127 " --> pdb=" O ALA f 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'f' and resid 161 through 162 Processing sheet with id=AH2, first strand: chain 'f' and resid 225 through 228 Processing sheet with id=AH3, first strand: chain 'f' and resid 309 through 312 removed outlier: 3.671A pdb=" N PHE f 310 " --> pdb=" O GLY f 334 " (cutoff:3.500A) 896 hydrogen bonds defined for protein. 2526 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: 6.56 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9102 1.33 - 1.45: 5898 1.45 - 1.57: 18636 1.57 - 1.68: 0 1.68 - 1.80: 192 Bond restraints: 33828 Sorted by residual: bond pdb=" C ILE E 95 " pdb=" N PRO E 96 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.91e+00 bond pdb=" C ILE f 95 " pdb=" N PRO f 96 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.88e+00 bond pdb=" C ILE D 95 " pdb=" N PRO D 96 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.88e+00 bond pdb=" C ILE d 95 " pdb=" N PRO d 96 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.28e-02 6.10e+03 1.87e+00 bond pdb=" CB THR d 240 " pdb=" CG2 THR d 240 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.76e+00 ... (remaining 33823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 45544 3.14 - 6.28: 452 6.28 - 9.42: 84 9.42 - 12.55: 12 12.55 - 15.69: 12 Bond angle restraints: 46104 Sorted by residual: angle pdb=" CA LEU e 125 " pdb=" CB LEU e 125 " pdb=" CG LEU e 125 " ideal model delta sigma weight residual 116.30 131.99 -15.69 3.50e+00 8.16e-02 2.01e+01 angle pdb=" CA LEU F 125 " pdb=" CB LEU F 125 " pdb=" CG LEU F 125 " ideal model delta sigma weight residual 116.30 131.99 -15.69 3.50e+00 8.16e-02 2.01e+01 angle pdb=" CA LEU b 125 " pdb=" CB LEU b 125 " pdb=" CG LEU b 125 " ideal model delta sigma weight residual 116.30 131.98 -15.68 3.50e+00 8.16e-02 2.01e+01 angle pdb=" CA LEU D 125 " pdb=" CB LEU D 125 " pdb=" CG LEU D 125 " ideal model delta sigma weight residual 116.30 131.98 -15.68 3.50e+00 8.16e-02 2.01e+01 angle pdb=" CA LEU A 125 " pdb=" CB LEU A 125 " pdb=" CG LEU A 125 " ideal model delta sigma weight residual 116.30 131.97 -15.67 3.50e+00 8.16e-02 2.00e+01 ... (remaining 46099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 17593 16.55 - 33.09: 1703 33.09 - 49.64: 504 49.64 - 66.18: 132 66.18 - 82.73: 84 Dihedral angle restraints: 20016 sinusoidal: 7692 harmonic: 12324 Sorted by residual: dihedral pdb=" CA PHE f 228 " pdb=" C PHE f 228 " pdb=" N SER f 229 " pdb=" CA SER f 229 " ideal model delta harmonic sigma weight residual 180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA PHE B 228 " pdb=" C PHE B 228 " pdb=" N SER B 229 " pdb=" CA SER B 229 " ideal model delta harmonic sigma weight residual -180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA PHE d 228 " pdb=" C PHE d 228 " pdb=" N SER d 229 " pdb=" CA SER d 229 " ideal model delta harmonic sigma weight residual 180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 20013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3073 0.038 - 0.075: 1373 0.075 - 0.113: 453 0.113 - 0.151: 219 0.151 - 0.188: 66 Chirality restraints: 5184 Sorted by residual: chirality pdb=" CA TYR F 158 " pdb=" N TYR F 158 " pdb=" C TYR F 158 " pdb=" CB TYR F 158 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CA TYR d 158 " pdb=" N TYR d 158 " pdb=" C TYR d 158 " pdb=" CB TYR d 158 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA TYR c 158 " pdb=" N TYR c 158 " pdb=" C TYR c 158 " pdb=" CB TYR c 158 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 5181 not shown) Planarity restraints: 5988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 120 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.61e+00 pdb=" N PRO a 121 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO a 121 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO a 121 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 120 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO C 121 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 120 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO E 121 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.038 5.00e-02 4.00e+02 ... (remaining 5985 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 10761 2.83 - 3.35: 29211 3.35 - 3.87: 53646 3.87 - 4.38: 58039 4.38 - 4.90: 101511 Nonbonded interactions: 253168 Sorted by model distance: nonbonded pdb=" O LYS d 67 " pdb=" OG SER d 71 " model vdw 2.313 3.040 nonbonded pdb=" O LYS A 67 " pdb=" OG SER A 71 " model vdw 2.313 3.040 nonbonded pdb=" O LYS B 67 " pdb=" OG SER B 71 " model vdw 2.313 3.040 nonbonded pdb=" O LYS F 67 " pdb=" OG SER F 71 " model vdw 2.313 3.040 nonbonded pdb=" O LYS f 67 " pdb=" OG SER f 71 " model vdw 2.313 3.040 ... (remaining 253163 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: 0.12 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 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 25.550 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.006 0.063 33828 Z= 0.273 Angle : 0.893 15.693 46104 Z= 0.464 Chirality : 0.053 0.188 5184 Planarity : 0.007 0.069 5988 Dihedral : 15.992 82.726 12120 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.09 % Allowed : 13.23 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.56 (0.09), residues: 4224 helix: -4.41 (0.05), residues: 1284 sheet: -1.70 (0.24), residues: 504 loop : -2.58 (0.09), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 48 TYR 0.015 0.003 TYR c 40 PHE 0.013 0.002 PHE D 348 TRP 0.019 0.002 TRP e 280 Details of bonding type rmsd covalent geometry : bond 0.00649 (33828) covalent geometry : angle 0.89262 (46104) hydrogen bonds : bond 0.32030 ( 896) hydrogen bonds : angle 9.94089 ( 2526) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1214 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.9091 (tp) cc_final: 0.8717 (mt) REVERT: A 248 ARG cc_start: 0.9005 (ttm170) cc_final: 0.8737 (ttm-80) REVERT: A 264 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8709 (ttpt) REVERT: B 47 ILE cc_start: 0.9069 (tp) cc_final: 0.8656 (mt) REVERT: B 118 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8485 (tm) REVERT: B 243 ASP cc_start: 0.7427 (t0) cc_final: 0.7196 (t0) REVERT: B 264 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8574 (ttpt) REVERT: C 47 ILE cc_start: 0.9002 (tp) cc_final: 0.8629 (mt) REVERT: C 73 ARG cc_start: 0.8727 (tpt-90) cc_final: 0.8369 (tmt-80) REVERT: C 118 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8337 (tm) REVERT: C 264 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8417 (ttpp) REVERT: C 309 TYR cc_start: 0.8529 (p90) cc_final: 0.8262 (p90) REVERT: C 329 MET cc_start: 0.8885 (ptt) cc_final: 0.8417 (ptm) REVERT: C 345 ILE cc_start: 0.8747 (pt) cc_final: 0.8531 (mt) REVERT: D 180 TYR cc_start: 0.9054 (m-10) cc_final: 0.8596 (m-10) REVERT: D 267 MET cc_start: 0.8828 (mmt) cc_final: 0.8564 (mmp) REVERT: D 345 ILE cc_start: 0.8908 (pt) cc_final: 0.8598 (mt) REVERT: E 47 ILE cc_start: 0.8985 (tp) cc_final: 0.8608 (mt) REVERT: E 73 ARG cc_start: 0.8744 (tpt-90) cc_final: 0.8518 (tpt170) REVERT: E 118 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8624 (tm) REVERT: E 136 LEU cc_start: 0.6655 (mp) cc_final: 0.6390 (tp) REVERT: E 243 ASP cc_start: 0.7446 (t0) cc_final: 0.7199 (t0) REVERT: E 264 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8590 (ttpt) REVERT: F 47 ILE cc_start: 0.9071 (tp) cc_final: 0.8701 (mt) REVERT: F 65 GLU cc_start: 0.7826 (tp30) cc_final: 0.7541 (mm-30) REVERT: F 73 ARG cc_start: 0.8682 (tpt-90) cc_final: 0.8441 (tpt170) REVERT: F 118 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8404 (tm) REVERT: F 180 TYR cc_start: 0.8978 (m-10) cc_final: 0.8530 (m-10) REVERT: F 184 ASP cc_start: 0.7421 (m-30) cc_final: 0.6980 (m-30) REVERT: F 264 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8527 (ttpp) REVERT: F 329 MET cc_start: 0.8761 (ptt) cc_final: 0.8344 (ptm) REVERT: a 143 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7596 (tm-30) REVERT: a 205 LYS cc_start: 0.8257 (tttt) cc_final: 0.7910 (tttt) REVERT: a 210 ASP cc_start: 0.8383 (t70) cc_final: 0.8116 (t0) REVERT: a 220 ARG cc_start: 0.8741 (ptt-90) cc_final: 0.8323 (mtm180) REVERT: a 252 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.9019 (p) REVERT: a 281 GLU cc_start: 0.7828 (tp30) cc_final: 0.7164 (tp30) REVERT: b 116 ASP cc_start: 0.6264 (t0) cc_final: 0.5607 (m-30) REVERT: b 143 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7459 (tm-30) REVERT: b 220 ARG cc_start: 0.8629 (ptt-90) cc_final: 0.8363 (mtm180) REVERT: b 235 VAL cc_start: 0.9500 (m) cc_final: 0.9300 (t) REVERT: b 281 GLU cc_start: 0.7771 (tp30) cc_final: 0.7197 (tp30) REVERT: b 292 TYR cc_start: 0.8902 (t80) cc_final: 0.8561 (t80) REVERT: c 205 LYS cc_start: 0.8437 (tttt) cc_final: 0.8090 (tttt) REVERT: c 220 ARG cc_start: 0.8381 (ptt-90) cc_final: 0.7854 (mtm180) REVERT: c 276 ASN cc_start: 0.8708 (p0) cc_final: 0.8413 (p0) REVERT: c 278 PRO cc_start: 0.9195 (Cg_exo) cc_final: 0.8836 (Cg_endo) REVERT: c 281 GLU cc_start: 0.7904 (tp30) cc_final: 0.7569 (tp30) REVERT: c 332 LYS cc_start: 0.8366 (mtpp) cc_final: 0.8085 (mmtt) REVERT: d 143 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7397 (tm-30) REVERT: d 210 ASP cc_start: 0.8460 (t70) cc_final: 0.8136 (t0) REVERT: d 220 ARG cc_start: 0.8741 (ptt-90) cc_final: 0.8375 (mtm180) REVERT: d 252 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9099 (p) REVERT: d 281 GLU cc_start: 0.7960 (tp30) cc_final: 0.7397 (tp30) REVERT: d 325 ASP cc_start: 0.7663 (m-30) cc_final: 0.7405 (m-30) REVERT: e 116 ASP cc_start: 0.6137 (t0) cc_final: 0.5571 (m-30) REVERT: e 143 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7440 (tm-30) REVERT: e 220 ARG cc_start: 0.8664 (ptt-90) cc_final: 0.8447 (mtm180) REVERT: e 281 GLU cc_start: 0.7819 (tp30) cc_final: 0.7240 (tp30) REVERT: e 292 TYR cc_start: 0.8908 (t80) cc_final: 0.8555 (t80) REVERT: f 205 LYS cc_start: 0.8383 (tttt) cc_final: 0.8032 (tttt) REVERT: f 220 ARG cc_start: 0.8435 (ptt-90) cc_final: 0.7982 (mtm180) REVERT: f 276 ASN cc_start: 0.8754 (p0) cc_final: 0.8469 (p0) REVERT: f 278 PRO cc_start: 0.9212 (Cg_exo) cc_final: 0.8883 (Cg_endo) REVERT: f 281 GLU cc_start: 0.7864 (tp30) cc_final: 0.7461 (tp30) REVERT: f 332 LYS cc_start: 0.8363 (mtpp) cc_final: 0.8092 (mmtt) outliers start: 108 outliers final: 32 residues processed: 1281 average time/residue: 0.2419 time to fit residues: 476.6684 Evaluate side-chains 616 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 573 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 252 VAL Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 344 ILE Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 344 ILE Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 318 THR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 252 VAL Chi-restraints excluded: chain d residue 318 THR Chi-restraints excluded: chain d residue 344 ILE Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 344 ILE Chi-restraints excluded: chain f residue 118 LEU Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 318 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 0.4980 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 78 ASN A 195 ASN A 246 ASN B 57 ASN B 78 ASN B 195 ASN B 246 ASN C 57 ASN C 78 ASN C 195 ASN C 246 ASN C 321 GLN D 57 ASN D 78 ASN D 195 ASN D 246 ASN D 321 GLN E 57 ASN E 78 ASN E 195 ASN E 217 ASN E 246 ASN E 321 GLN F 57 ASN F 78 ASN F 195 ASN F 246 ASN a 78 ASN a 195 ASN a 223 ASN b 78 ASN b 195 ASN b 223 ASN c 78 ASN c 195 ASN c 223 ASN d 78 ASN d 195 ASN d 223 ASN d 246 ASN e 78 ASN e 195 ASN e 223 ASN f 78 ASN f 195 ASN f 223 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.105307 restraints weight = 51796.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.108059 restraints weight = 32663.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109929 restraints weight = 23439.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111226 restraints weight = 18350.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112147 restraints weight = 15269.789| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33828 Z= 0.126 Angle : 0.646 13.189 46104 Z= 0.330 Chirality : 0.044 0.165 5184 Planarity : 0.005 0.068 5988 Dihedral : 6.410 49.751 4690 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.61 % Allowed : 18.93 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.51 (0.11), residues: 4224 helix: -2.46 (0.11), residues: 1428 sheet: -2.35 (0.24), residues: 384 loop : -2.26 (0.10), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 254 TYR 0.023 0.001 TYR a 82 PHE 0.018 0.001 PHE d 348 TRP 0.015 0.001 TRP F 280 Details of bonding type rmsd covalent geometry : bond 0.00284 (33828) covalent geometry : angle 0.64600 (46104) hydrogen bonds : bond 0.04826 ( 896) hydrogen bonds : angle 5.34749 ( 2526) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 685 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8954 (tp) cc_final: 0.8732 (mt) REVERT: A 345 ILE cc_start: 0.8804 (pt) cc_final: 0.8584 (mt) REVERT: B 47 ILE cc_start: 0.8863 (tp) cc_final: 0.8607 (mt) REVERT: B 264 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8723 (ttpt) REVERT: B 271 MET cc_start: 0.9260 (tpt) cc_final: 0.9043 (tpt) REVERT: B 305 GLU cc_start: 0.7590 (pt0) cc_final: 0.7264 (tt0) REVERT: C 47 ILE cc_start: 0.8955 (tp) cc_final: 0.8726 (mt) REVERT: C 118 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8532 (tm) REVERT: C 264 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8727 (ttmt) REVERT: C 305 GLU cc_start: 0.7557 (pt0) cc_final: 0.7052 (tt0) REVERT: C 329 MET cc_start: 0.8889 (ptt) cc_final: 0.8556 (ptm) REVERT: D 47 ILE cc_start: 0.8972 (tp) cc_final: 0.8769 (mt) REVERT: D 180 TYR cc_start: 0.8892 (m-10) cc_final: 0.8441 (m-10) REVERT: D 325 ASP cc_start: 0.8403 (m-30) cc_final: 0.7582 (m-30) REVERT: D 345 ILE cc_start: 0.8835 (pt) cc_final: 0.8607 (mt) REVERT: E 47 ILE cc_start: 0.8932 (tp) cc_final: 0.8695 (mt) REVERT: E 217 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8738 (t0) REVERT: E 264 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8712 (ttpt) REVERT: F 47 ILE cc_start: 0.8955 (tp) cc_final: 0.8738 (mt) REVERT: F 118 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8532 (tm) REVERT: F 184 ASP cc_start: 0.7059 (m-30) cc_final: 0.6834 (m-30) REVERT: F 264 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8655 (ttpp) REVERT: F 305 GLU cc_start: 0.7607 (pt0) cc_final: 0.7134 (tt0) REVERT: F 329 MET cc_start: 0.8790 (ptt) cc_final: 0.8520 (ptm) REVERT: a 72 VAL cc_start: 0.9248 (p) cc_final: 0.8950 (t) REVERT: a 260 GLU cc_start: 0.6190 (mm-30) cc_final: 0.5385 (mm-30) REVERT: a 292 TYR cc_start: 0.8706 (t80) cc_final: 0.8426 (t80) REVERT: b 72 VAL cc_start: 0.9169 (p) cc_final: 0.8791 (t) REVERT: b 82 TYR cc_start: 0.8347 (p90) cc_final: 0.8118 (p90) REVERT: b 116 ASP cc_start: 0.5854 (t0) cc_final: 0.5536 (m-30) REVERT: b 260 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6360 (mm-30) REVERT: b 271 MET cc_start: 0.8545 (tpt) cc_final: 0.8316 (tpt) REVERT: b 329 MET cc_start: 0.8485 (ptt) cc_final: 0.8078 (ptm) REVERT: c 72 VAL cc_start: 0.9258 (p) cc_final: 0.9049 (t) REVERT: c 260 GLU cc_start: 0.6358 (mm-30) cc_final: 0.6099 (mm-30) REVERT: d 72 VAL cc_start: 0.9242 (p) cc_final: 0.8931 (t) REVERT: d 260 GLU cc_start: 0.6187 (mm-30) cc_final: 0.5319 (mm-30) REVERT: e 72 VAL cc_start: 0.9116 (p) cc_final: 0.8750 (t) REVERT: e 82 TYR cc_start: 0.8339 (p90) cc_final: 0.8096 (p90) REVERT: e 116 ASP cc_start: 0.5805 (t0) cc_final: 0.5524 (m-30) REVERT: e 169 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7104 (t0) REVERT: e 224 MET cc_start: 0.8410 (mmm) cc_final: 0.8202 (mmt) REVERT: e 260 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6136 (mm-30) REVERT: e 329 MET cc_start: 0.8476 (ptt) cc_final: 0.8193 (ptm) REVERT: f 72 VAL cc_start: 0.9246 (p) cc_final: 0.9046 (t) REVERT: f 210 ASP cc_start: 0.8571 (t0) cc_final: 0.8362 (t0) REVERT: f 260 GLU cc_start: 0.6362 (mm-30) cc_final: 0.5927 (mm-30) REVERT: f 271 MET cc_start: 0.7928 (tpt) cc_final: 0.7653 (tpt) outliers start: 126 outliers final: 57 residues processed: 772 average time/residue: 0.2093 time to fit residues: 267.2081 Evaluate side-chains 614 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 549 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 217 ASN Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 344 ILE Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 235 VAL Chi-restraints excluded: chain d residue 344 ILE Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 344 ILE Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 118 LEU Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 250 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 64 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 189 optimal weight: 0.0060 chunk 286 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 383 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 overall best weight: 5.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN C 63 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN E 63 ASN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN E 321 GLN F 63 ASN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 ASN F 321 GLN b 57 ASN c 57 ASN c 350 GLN e 57 ASN f 57 ASN f 350 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.111108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.095810 restraints weight = 53033.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.098110 restraints weight = 35323.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.099722 restraints weight = 26472.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.100836 restraints weight = 21396.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.101610 restraints weight = 18252.684| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 33828 Z= 0.298 Angle : 0.759 15.193 46104 Z= 0.380 Chirality : 0.050 0.163 5184 Planarity : 0.005 0.046 5988 Dihedral : 6.253 51.858 4664 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.64 % Allowed : 19.53 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.11), residues: 4224 helix: -1.34 (0.13), residues: 1428 sheet: -2.53 (0.24), residues: 408 loop : -1.93 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 284 TYR 0.028 0.002 TYR f 292 PHE 0.022 0.002 PHE c 348 TRP 0.019 0.002 TRP e 280 Details of bonding type rmsd covalent geometry : bond 0.00723 (33828) covalent geometry : angle 0.75930 (46104) hydrogen bonds : bond 0.05183 ( 896) hydrogen bonds : angle 4.93958 ( 2526) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 534 time to evaluate : 1.333 Fit side-chains REVERT: A 47 ILE cc_start: 0.8871 (tp) cc_final: 0.8656 (mt) REVERT: B 47 ILE cc_start: 0.8842 (tp) cc_final: 0.8632 (mt) REVERT: B 264 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8756 (ttpt) REVERT: C 118 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8859 (tm) REVERT: C 264 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8657 (ttpp) REVERT: C 305 GLU cc_start: 0.7574 (pt0) cc_final: 0.7183 (tt0) REVERT: C 329 MET cc_start: 0.8870 (ptt) cc_final: 0.8558 (ptm) REVERT: C 344 ILE cc_start: 0.9546 (OUTLIER) cc_final: 0.9243 (mt) REVERT: D 23 SER cc_start: 0.8458 (p) cc_final: 0.8161 (m) REVERT: D 180 TYR cc_start: 0.8842 (m-10) cc_final: 0.8562 (m-10) REVERT: D 216 TYR cc_start: 0.8925 (m-80) cc_final: 0.8689 (m-10) REVERT: E 23 SER cc_start: 0.8587 (p) cc_final: 0.8180 (m) REVERT: E 264 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8661 (ttpp) REVERT: E 271 MET cc_start: 0.9239 (tpt) cc_final: 0.9016 (tpt) REVERT: F 118 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8790 (tm) REVERT: F 264 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8686 (ttpp) REVERT: F 305 GLU cc_start: 0.7681 (pt0) cc_final: 0.7215 (tt0) REVERT: F 329 MET cc_start: 0.8876 (ptt) cc_final: 0.8571 (ptm) REVERT: a 235 VAL cc_start: 0.9600 (m) cc_final: 0.9301 (t) REVERT: a 260 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6383 (mm-30) REVERT: a 271 MET cc_start: 0.8669 (tpt) cc_final: 0.8431 (tpt) REVERT: b 116 ASP cc_start: 0.6032 (t0) cc_final: 0.5695 (m-30) REVERT: b 260 GLU cc_start: 0.6454 (mm-30) cc_final: 0.5856 (mm-30) REVERT: b 329 MET cc_start: 0.8641 (ptt) cc_final: 0.8432 (ptm) REVERT: c 260 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6189 (mm-30) REVERT: c 304 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7978 (pttm) REVERT: d 260 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6619 (mm-30) REVERT: d 271 MET cc_start: 0.8724 (tpt) cc_final: 0.8490 (tpt) REVERT: d 292 TYR cc_start: 0.8810 (t80) cc_final: 0.8554 (t80) REVERT: e 116 ASP cc_start: 0.5971 (t0) cc_final: 0.5667 (m-30) REVERT: e 260 GLU cc_start: 0.6560 (mm-30) cc_final: 0.5831 (mm-30) REVERT: e 292 TYR cc_start: 0.8968 (t80) cc_final: 0.8620 (t80) REVERT: e 329 MET cc_start: 0.8576 (ptt) cc_final: 0.8342 (ptm) REVERT: f 260 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6263 (mm-30) REVERT: f 304 LYS cc_start: 0.8551 (pttm) cc_final: 0.8306 (pttm) outliers start: 197 outliers final: 112 residues processed: 680 average time/residue: 0.2088 time to fit residues: 234.8802 Evaluate side-chains 572 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 452 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 99 ASP Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 279 THR Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain a residue 344 ILE Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 99 ASP Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 203 GLU Chi-restraints excluded: chain c residue 234 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 294 LEU Chi-restraints excluded: chain c residue 304 LYS Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 203 GLU Chi-restraints excluded: chain d residue 234 THR Chi-restraints excluded: chain d residue 279 THR Chi-restraints excluded: chain d residue 294 LEU Chi-restraints excluded: chain d residue 305 GLU Chi-restraints excluded: chain d residue 306 GLU Chi-restraints excluded: chain d residue 344 ILE Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain e residue 344 ILE Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 118 LEU Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 203 GLU Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 294 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 121 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 chunk 312 optimal weight: 4.9990 chunk 374 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 78 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN d 45 ASN e 57 ASN e 63 ASN f 350 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.097321 restraints weight = 52474.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.099675 restraints weight = 34682.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.101286 restraints weight = 25840.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.102463 restraints weight = 20826.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.103321 restraints weight = 17643.667| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33828 Z= 0.177 Angle : 0.655 14.952 46104 Z= 0.323 Chirality : 0.046 0.259 5184 Planarity : 0.004 0.046 5988 Dihedral : 5.913 52.027 4662 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.78 % Allowed : 22.45 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.12), residues: 4224 helix: -0.65 (0.14), residues: 1428 sheet: -2.61 (0.24), residues: 408 loop : -1.81 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 284 TYR 0.020 0.001 TYR A 216 PHE 0.014 0.001 PHE e 348 TRP 0.015 0.001 TRP F 52 Details of bonding type rmsd covalent geometry : bond 0.00431 (33828) covalent geometry : angle 0.65536 (46104) hydrogen bonds : bond 0.04130 ( 896) hydrogen bonds : angle 4.61522 ( 2526) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 501 time to evaluate : 1.299 Fit side-chains REVERT: A 315 LYS cc_start: 0.9151 (ttmm) cc_final: 0.8825 (ttpt) REVERT: B 23 SER cc_start: 0.8624 (p) cc_final: 0.8192 (m) REVERT: B 264 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8639 (ttpp) REVERT: B 271 MET cc_start: 0.9229 (tpt) cc_final: 0.8984 (tpt) REVERT: C 118 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8866 (tm) REVERT: C 215 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6171 (tt0) REVERT: C 264 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8496 (ttpp) REVERT: C 305 GLU cc_start: 0.7579 (pt0) cc_final: 0.7134 (tt0) REVERT: C 329 MET cc_start: 0.8878 (ptt) cc_final: 0.8533 (ptm) REVERT: C 344 ILE cc_start: 0.9525 (OUTLIER) cc_final: 0.9315 (mt) REVERT: D 23 SER cc_start: 0.8496 (p) cc_final: 0.8188 (m) REVERT: D 180 TYR cc_start: 0.8773 (m-10) cc_final: 0.8562 (m-10) REVERT: D 315 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8888 (ttpt) REVERT: D 325 ASP cc_start: 0.8376 (m-30) cc_final: 0.8099 (m-30) REVERT: E 23 SER cc_start: 0.8555 (p) cc_final: 0.8105 (m) REVERT: E 264 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8550 (ttpp) REVERT: E 271 MET cc_start: 0.9214 (tpt) cc_final: 0.8998 (tpt) REVERT: E 290 TYR cc_start: 0.9039 (t80) cc_final: 0.8816 (t80) REVERT: F 215 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6254 (tt0) REVERT: F 264 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8559 (ttpp) REVERT: F 304 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8018 (pttm) REVERT: F 306 GLU cc_start: 0.7762 (pt0) cc_final: 0.7396 (pt0) REVERT: F 329 MET cc_start: 0.8863 (ptt) cc_final: 0.8516 (ptm) REVERT: a 72 VAL cc_start: 0.9280 (p) cc_final: 0.8898 (t) REVERT: a 243 ASP cc_start: 0.7337 (t0) cc_final: 0.7122 (t70) REVERT: a 260 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6120 (mm-30) REVERT: b 72 VAL cc_start: 0.9164 (p) cc_final: 0.8817 (t) REVERT: b 116 ASP cc_start: 0.6059 (t0) cc_final: 0.5800 (m-30) REVERT: b 260 GLU cc_start: 0.6319 (mm-30) cc_final: 0.4987 (pt0) REVERT: c 235 VAL cc_start: 0.9621 (m) cc_final: 0.9332 (t) REVERT: c 260 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6038 (mm-30) REVERT: c 304 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8125 (pttm) REVERT: d 72 VAL cc_start: 0.9285 (p) cc_final: 0.8940 (t) REVERT: d 260 GLU cc_start: 0.6773 (mm-30) cc_final: 0.5984 (mm-30) REVERT: e 72 VAL cc_start: 0.9188 (p) cc_final: 0.8824 (t) REVERT: e 116 ASP cc_start: 0.5992 (t0) cc_final: 0.5775 (m-30) REVERT: e 224 MET cc_start: 0.8353 (mmm) cc_final: 0.7984 (mmt) REVERT: e 260 GLU cc_start: 0.6404 (mm-30) cc_final: 0.5680 (mm-30) REVERT: f 235 VAL cc_start: 0.9607 (m) cc_final: 0.9324 (t) REVERT: f 260 GLU cc_start: 0.6717 (mm-30) cc_final: 0.5979 (mm-30) outliers start: 167 outliers final: 102 residues processed: 624 average time/residue: 0.1963 time to fit residues: 207.6076 Evaluate side-chains 557 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 445 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 99 ASP Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 203 GLU Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain a residue 305 GLU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 203 GLU Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 234 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 294 LEU Chi-restraints excluded: chain c residue 304 LYS Chi-restraints excluded: chain c residue 305 GLU Chi-restraints excluded: chain c residue 318 THR Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 203 GLU Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain d residue 234 THR Chi-restraints excluded: chain d residue 306 GLU Chi-restraints excluded: chain d residue 344 ILE Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 203 GLU Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 118 LEU Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 294 LEU Chi-restraints excluded: chain f residue 318 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 108 optimal weight: 0.4980 chunk 249 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 38 optimal weight: 0.0670 chunk 279 optimal weight: 7.9990 chunk 280 optimal weight: 0.9980 chunk 308 optimal weight: 7.9990 chunk 184 optimal weight: 0.8980 chunk 304 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 363 optimal weight: 10.0000 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN C 321 GLN D 321 GLN a 45 ASN f 45 ASN f 350 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.102698 restraints weight = 51866.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.104805 restraints weight = 35676.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106280 restraints weight = 27207.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.107267 restraints weight = 22226.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108056 restraints weight = 19153.762| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 33828 Z= 0.104 Angle : 0.605 13.431 46104 Z= 0.292 Chirality : 0.044 0.319 5184 Planarity : 0.004 0.042 5988 Dihedral : 5.332 51.050 4654 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.04 % Allowed : 23.11 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.12), residues: 4224 helix: -0.01 (0.15), residues: 1248 sheet: -2.54 (0.24), residues: 408 loop : -1.62 (0.11), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 284 TYR 0.016 0.001 TYR b 40 PHE 0.020 0.001 PHE a 348 TRP 0.018 0.001 TRP A 280 Details of bonding type rmsd covalent geometry : bond 0.00242 (33828) covalent geometry : angle 0.60549 (46104) hydrogen bonds : bond 0.03423 ( 896) hydrogen bonds : angle 4.30336 ( 2526) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 539 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 72 VAL cc_start: 0.9325 (p) cc_final: 0.9050 (t) REVERT: A 304 LYS cc_start: 0.8417 (pttm) cc_final: 0.7930 (pttm) REVERT: A 315 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8805 (tttm) REVERT: B 264 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8612 (ttpt) REVERT: B 271 MET cc_start: 0.9292 (tpt) cc_final: 0.9065 (tpt) REVERT: B 273 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8009 (mm-30) REVERT: C 264 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8513 (ttpp) REVERT: C 305 GLU cc_start: 0.7482 (pt0) cc_final: 0.7218 (tt0) REVERT: D 23 SER cc_start: 0.8449 (p) cc_final: 0.8188 (m) REVERT: D 72 VAL cc_start: 0.9313 (p) cc_final: 0.8985 (t) REVERT: E 264 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8605 (ttpt) REVERT: F 345 ILE cc_start: 0.8567 (pt) cc_final: 0.8367 (mt) REVERT: a 260 GLU cc_start: 0.6501 (mm-30) cc_final: 0.5817 (mm-30) REVERT: b 72 VAL cc_start: 0.9116 (p) cc_final: 0.8874 (t) REVERT: b 235 VAL cc_start: 0.9561 (m) cc_final: 0.9187 (t) REVERT: b 260 GLU cc_start: 0.6557 (mm-30) cc_final: 0.5372 (pt0) REVERT: c 235 VAL cc_start: 0.9591 (m) cc_final: 0.9301 (t) REVERT: c 260 GLU cc_start: 0.6518 (mm-30) cc_final: 0.5785 (mm-30) REVERT: d 260 GLU cc_start: 0.6487 (mm-30) cc_final: 0.5683 (mm-30) REVERT: e 72 VAL cc_start: 0.9154 (p) cc_final: 0.8895 (t) REVERT: e 235 VAL cc_start: 0.9539 (m) cc_final: 0.9174 (t) REVERT: e 260 GLU cc_start: 0.6636 (mm-30) cc_final: 0.5565 (pt0) REVERT: f 235 VAL cc_start: 0.9602 (m) cc_final: 0.9321 (t) REVERT: f 260 GLU cc_start: 0.6471 (mm-30) cc_final: 0.5730 (mm-30) outliers start: 141 outliers final: 78 residues processed: 644 average time/residue: 0.1907 time to fit residues: 209.3378 Evaluate side-chains 532 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 450 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 228 PHE Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 228 PHE Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 215 GLU Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain d residue 245 ASP Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain f residue 53 MET Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 118 LEU Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 306 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 372 optimal weight: 9.9990 chunk 332 optimal weight: 0.5980 chunk 322 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 233 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 194 optimal weight: 9.9990 chunk 369 optimal weight: 10.0000 chunk 14 optimal weight: 0.0970 chunk 149 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 45 ASN e 45 ASN f 350 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.117079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.102442 restraints weight = 51833.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.104823 restraints weight = 33639.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.106472 restraints weight = 24725.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.107634 restraints weight = 19703.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.108458 restraints weight = 16581.047| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33828 Z= 0.102 Angle : 0.623 15.701 46104 Z= 0.292 Chirality : 0.044 0.206 5184 Planarity : 0.004 0.043 5988 Dihedral : 4.985 49.407 4644 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.15 % Allowed : 23.91 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.12), residues: 4224 helix: 0.30 (0.15), residues: 1260 sheet: -2.31 (0.25), residues: 384 loop : -1.53 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 284 TYR 0.019 0.001 TYR a 292 PHE 0.020 0.001 PHE a 348 TRP 0.026 0.001 TRP D 280 Details of bonding type rmsd covalent geometry : bond 0.00238 (33828) covalent geometry : angle 0.62298 (46104) hydrogen bonds : bond 0.03237 ( 896) hydrogen bonds : angle 4.14226 ( 2526) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 526 time to evaluate : 1.133 Fit side-chains REVERT: A 23 SER cc_start: 0.8277 (p) cc_final: 0.7908 (m) REVERT: A 72 VAL cc_start: 0.9272 (p) cc_final: 0.9025 (t) REVERT: B 264 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8429 (ttpp) REVERT: B 273 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: B 319 MET cc_start: 0.8735 (ptp) cc_final: 0.8467 (ptp) REVERT: C 264 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8530 (ttpp) REVERT: C 305 GLU cc_start: 0.7475 (pt0) cc_final: 0.7229 (tt0) REVERT: D 23 SER cc_start: 0.8446 (p) cc_final: 0.8161 (m) REVERT: D 72 VAL cc_start: 0.9284 (p) cc_final: 0.8961 (t) REVERT: D 305 GLU cc_start: 0.7508 (pt0) cc_final: 0.7163 (tt0) REVERT: E 264 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8432 (ttpp) REVERT: E 273 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8025 (mm-30) REVERT: F 23 SER cc_start: 0.8146 (p) cc_final: 0.7914 (m) REVERT: F 72 VAL cc_start: 0.9262 (p) cc_final: 0.8909 (t) REVERT: a 5 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8390 (p) REVERT: a 260 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6027 (mm-30) REVERT: b 72 VAL cc_start: 0.9099 (p) cc_final: 0.8852 (t) REVERT: b 235 VAL cc_start: 0.9566 (m) cc_final: 0.9193 (t) REVERT: b 260 GLU cc_start: 0.6727 (mm-30) cc_final: 0.5397 (pt0) REVERT: c 13 GLU cc_start: 0.7065 (pt0) cc_final: 0.6776 (pt0) REVERT: c 235 VAL cc_start: 0.9617 (m) cc_final: 0.9242 (t) REVERT: c 260 GLU cc_start: 0.6624 (mm-30) cc_final: 0.6068 (mm-30) REVERT: d 260 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6041 (mm-30) REVERT: e 72 VAL cc_start: 0.9071 (p) cc_final: 0.8853 (t) REVERT: e 235 VAL cc_start: 0.9556 (m) cc_final: 0.9187 (t) REVERT: e 260 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6033 (mm-30) REVERT: f 235 VAL cc_start: 0.9619 (m) cc_final: 0.9300 (t) REVERT: f 260 GLU cc_start: 0.6550 (mm-30) cc_final: 0.5864 (mm-30) outliers start: 110 outliers final: 72 residues processed: 598 average time/residue: 0.1929 time to fit residues: 197.3900 Evaluate side-chains 538 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 461 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 203 GLU Chi-restraints excluded: chain a residue 228 PHE Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 228 PHE Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 215 GLU Chi-restraints excluded: chain c residue 234 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 305 GLU Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 176 MET Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 306 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 125 optimal weight: 0.0470 chunk 370 optimal weight: 20.0000 chunk 200 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 415 optimal weight: 0.0570 chunk 414 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 374 optimal weight: 1.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN B 297 GLN C 321 GLN D 321 GLN E 297 GLN a 63 ASN a 276 ASN d 276 ASN f 63 ASN f 350 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.103255 restraints weight = 51802.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.105606 restraints weight = 33643.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.107247 restraints weight = 24732.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.108404 restraints weight = 19671.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.109215 restraints weight = 16554.169| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33828 Z= 0.101 Angle : 0.610 15.466 46104 Z= 0.287 Chirality : 0.044 0.177 5184 Planarity : 0.004 0.042 5988 Dihedral : 4.718 48.615 4632 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.06 % Allowed : 24.17 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.13), residues: 4224 helix: 0.44 (0.15), residues: 1272 sheet: -2.13 (0.26), residues: 384 loop : -1.47 (0.11), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 284 TYR 0.015 0.001 TYR e 309 PHE 0.015 0.001 PHE a 348 TRP 0.019 0.001 TRP A 280 Details of bonding type rmsd covalent geometry : bond 0.00233 (33828) covalent geometry : angle 0.61009 (46104) hydrogen bonds : bond 0.03122 ( 896) hydrogen bonds : angle 4.04950 ( 2526) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 507 time to evaluate : 1.436 Fit side-chains REVERT: A 23 SER cc_start: 0.8220 (p) cc_final: 0.7892 (m) REVERT: A 72 VAL cc_start: 0.9277 (p) cc_final: 0.9036 (t) REVERT: A 264 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8463 (ttpp) REVERT: B 203 GLU cc_start: 0.7616 (pt0) cc_final: 0.7258 (mp0) REVERT: B 273 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: C 305 GLU cc_start: 0.7489 (pt0) cc_final: 0.7215 (tt0) REVERT: D 23 SER cc_start: 0.8509 (p) cc_final: 0.8246 (m) REVERT: D 72 VAL cc_start: 0.9286 (p) cc_final: 0.8935 (t) REVERT: D 344 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9189 (mt) REVERT: F 72 VAL cc_start: 0.9259 (p) cc_final: 0.8892 (t) REVERT: F 304 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8102 (pttm) REVERT: F 321 GLN cc_start: 0.8601 (tp40) cc_final: 0.8251 (tp-100) REVERT: F 325 ASP cc_start: 0.8187 (m-30) cc_final: 0.7900 (m-30) REVERT: a 5 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8356 (p) REVERT: a 260 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6063 (mm-30) REVERT: a 304 LYS cc_start: 0.8632 (pttm) cc_final: 0.8337 (pttm) REVERT: b 72 VAL cc_start: 0.9099 (p) cc_final: 0.8812 (t) REVERT: b 235 VAL cc_start: 0.9564 (m) cc_final: 0.9185 (t) REVERT: b 260 GLU cc_start: 0.6735 (mm-30) cc_final: 0.5445 (pt0) REVERT: c 13 GLU cc_start: 0.6983 (pt0) cc_final: 0.6711 (pt0) REVERT: c 260 GLU cc_start: 0.6540 (mm-30) cc_final: 0.5890 (mm-30) REVERT: d 220 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8150 (mtm180) REVERT: d 260 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6120 (mm-30) REVERT: e 72 VAL cc_start: 0.9095 (p) cc_final: 0.8849 (t) REVERT: e 235 VAL cc_start: 0.9567 (m) cc_final: 0.9188 (t) REVERT: e 260 GLU cc_start: 0.6784 (mm-30) cc_final: 0.5607 (pt0) REVERT: f 5 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8020 (p) REVERT: f 235 VAL cc_start: 0.9602 (m) cc_final: 0.9269 (t) REVERT: f 260 GLU cc_start: 0.6547 (mm-30) cc_final: 0.5868 (mm-30) outliers start: 107 outliers final: 72 residues processed: 575 average time/residue: 0.1871 time to fit residues: 186.0157 Evaluate side-chains 547 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 468 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 99 ASP Chi-restraints excluded: chain a residue 228 PHE Chi-restraints excluded: chain a residue 235 VAL Chi-restraints excluded: chain a residue 276 ASN Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 228 PHE Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 215 GLU Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 142 GLU Chi-restraints excluded: chain d residue 220 ARG Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain d residue 276 ASN Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 250 VAL Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 253 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 355 optimal weight: 1.9990 chunk 382 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 311 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 250 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 276 ASN a 277 GLN b 276 ASN d 276 ASN d 277 GLN e 276 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.101993 restraints weight = 51675.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.104342 restraints weight = 33833.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.105961 restraints weight = 24972.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.107059 restraints weight = 19990.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.107901 restraints weight = 16992.454| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33828 Z= 0.122 Angle : 0.624 16.227 46104 Z= 0.293 Chirality : 0.044 0.169 5184 Planarity : 0.004 0.045 5988 Dihedral : 4.571 29.906 4620 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.04 % Allowed : 24.46 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.13), residues: 4224 helix: 0.53 (0.15), residues: 1272 sheet: -2.04 (0.26), residues: 384 loop : -1.46 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 284 TYR 0.021 0.001 TYR A 216 PHE 0.016 0.001 PHE a 348 TRP 0.020 0.001 TRP D 280 Details of bonding type rmsd covalent geometry : bond 0.00296 (33828) covalent geometry : angle 0.62441 (46104) hydrogen bonds : bond 0.03204 ( 896) hydrogen bonds : angle 4.04293 ( 2526) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 468 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: A 23 SER cc_start: 0.8303 (p) cc_final: 0.8015 (m) REVERT: A 72 VAL cc_start: 0.9290 (p) cc_final: 0.9030 (t) REVERT: B 203 GLU cc_start: 0.7631 (pt0) cc_final: 0.7257 (mp0) REVERT: B 271 MET cc_start: 0.9246 (tpt) cc_final: 0.8961 (tpt) REVERT: B 273 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8050 (mm-30) REVERT: C 305 GLU cc_start: 0.7530 (pt0) cc_final: 0.7238 (tt0) REVERT: D 23 SER cc_start: 0.8513 (p) cc_final: 0.8267 (m) REVERT: D 344 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9227 (mt) REVERT: E 23 SER cc_start: 0.8476 (p) cc_final: 0.8094 (m) REVERT: F 224 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7895 (mtp) REVERT: F 305 GLU cc_start: 0.7534 (pt0) cc_final: 0.7224 (tt0) REVERT: a 5 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8387 (p) REVERT: a 220 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8139 (mtm180) REVERT: a 260 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6135 (mm-30) REVERT: a 304 LYS cc_start: 0.8652 (pttm) cc_final: 0.8361 (pttm) REVERT: b 72 VAL cc_start: 0.9086 (p) cc_final: 0.8785 (t) REVERT: b 235 VAL cc_start: 0.9575 (OUTLIER) cc_final: 0.9201 (t) REVERT: b 260 GLU cc_start: 0.6407 (mm-30) cc_final: 0.5145 (pt0) REVERT: c 13 GLU cc_start: 0.7022 (pt0) cc_final: 0.6739 (pt0) REVERT: c 176 MET cc_start: 0.8848 (mmm) cc_final: 0.8384 (tpp) REVERT: c 260 GLU cc_start: 0.6470 (mm-30) cc_final: 0.5742 (mm-30) REVERT: d 220 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8183 (mtm180) REVERT: d 260 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6108 (mm-30) REVERT: e 72 VAL cc_start: 0.9117 (p) cc_final: 0.8821 (t) REVERT: e 235 VAL cc_start: 0.9569 (OUTLIER) cc_final: 0.9193 (t) REVERT: e 260 GLU cc_start: 0.6812 (mm-30) cc_final: 0.5515 (pt0) REVERT: f 5 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8152 (p) REVERT: f 235 VAL cc_start: 0.9600 (m) cc_final: 0.9260 (t) REVERT: f 260 GLU cc_start: 0.6457 (mm-30) cc_final: 0.5723 (mm-30) outliers start: 106 outliers final: 82 residues processed: 531 average time/residue: 0.1929 time to fit residues: 176.1715 Evaluate side-chains 546 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 455 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 99 ASP Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 203 GLU Chi-restraints excluded: chain a residue 220 ARG Chi-restraints excluded: chain a residue 228 PHE Chi-restraints excluded: chain a residue 235 VAL Chi-restraints excluded: chain a residue 276 ASN Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 228 PHE Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 203 GLU Chi-restraints excluded: chain c residue 215 GLU Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 142 GLU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 220 ARG Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain d residue 276 ASN Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 176 MET Chi-restraints excluded: chain e residue 203 GLU Chi-restraints excluded: chain e residue 234 THR Chi-restraints excluded: chain e residue 235 VAL Chi-restraints excluded: chain e residue 250 VAL Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 306 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 306 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 230 optimal weight: 0.0060 chunk 296 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN F 321 GLN a 276 ASN b 276 ASN c 276 ASN d 276 ASN e 276 ASN f 276 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.103245 restraints weight = 51418.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105613 restraints weight = 33551.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.107235 restraints weight = 24669.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.108403 restraints weight = 19645.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.109230 restraints weight = 16572.371| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33828 Z= 0.103 Angle : 0.619 15.974 46104 Z= 0.289 Chirality : 0.044 0.156 5184 Planarity : 0.004 0.042 5988 Dihedral : 4.512 29.493 4620 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.84 % Allowed : 24.63 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.13), residues: 4224 helix: 0.74 (0.15), residues: 1248 sheet: -2.03 (0.26), residues: 384 loop : -1.44 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 284 TYR 0.023 0.001 TYR F 292 PHE 0.012 0.001 PHE a 348 TRP 0.019 0.001 TRP D 280 Details of bonding type rmsd covalent geometry : bond 0.00240 (33828) covalent geometry : angle 0.61891 (46104) hydrogen bonds : bond 0.03083 ( 896) hydrogen bonds : angle 4.01261 ( 2526) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 500 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 23 SER cc_start: 0.8296 (p) cc_final: 0.8017 (m) REVERT: A 72 VAL cc_start: 0.9234 (p) cc_final: 0.9002 (t) REVERT: B 203 GLU cc_start: 0.7657 (pt0) cc_final: 0.7243 (mp0) REVERT: B 271 MET cc_start: 0.9221 (tpt) cc_final: 0.8991 (tpt) REVERT: B 273 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: C 305 GLU cc_start: 0.7549 (pt0) cc_final: 0.7216 (tt0) REVERT: D 23 SER cc_start: 0.8561 (p) cc_final: 0.8297 (m) REVERT: E 23 SER cc_start: 0.8486 (p) cc_final: 0.8083 (m) REVERT: F 305 GLU cc_start: 0.7577 (pt0) cc_final: 0.7259 (tt0) REVERT: a 5 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8415 (p) REVERT: a 220 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8028 (mtm180) REVERT: a 260 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6072 (mm-30) REVERT: a 304 LYS cc_start: 0.8686 (pttm) cc_final: 0.8421 (pttm) REVERT: b 72 VAL cc_start: 0.9028 (p) cc_final: 0.8731 (t) REVERT: b 235 VAL cc_start: 0.9569 (OUTLIER) cc_final: 0.9179 (t) REVERT: b 260 GLU cc_start: 0.6729 (mm-30) cc_final: 0.5300 (pt0) REVERT: c 260 GLU cc_start: 0.6655 (mm-30) cc_final: 0.6007 (mm-30) REVERT: d 260 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6071 (mm-30) REVERT: e 72 VAL cc_start: 0.9040 (p) cc_final: 0.8766 (t) REVERT: e 235 VAL cc_start: 0.9568 (OUTLIER) cc_final: 0.9196 (t) REVERT: e 260 GLU cc_start: 0.6753 (mm-30) cc_final: 0.5419 (pt0) REVERT: f 5 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8263 (p) REVERT: f 235 VAL cc_start: 0.9576 (m) cc_final: 0.9255 (t) REVERT: f 260 GLU cc_start: 0.6422 (mm-30) cc_final: 0.5706 (mm-30) outliers start: 99 outliers final: 78 residues processed: 553 average time/residue: 0.1933 time to fit residues: 183.8989 Evaluate side-chains 552 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 468 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 99 ASP Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 203 GLU Chi-restraints excluded: chain a residue 220 ARG Chi-restraints excluded: chain a residue 228 PHE Chi-restraints excluded: chain a residue 235 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 228 PHE Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 203 GLU Chi-restraints excluded: chain c residue 215 GLU Chi-restraints excluded: chain c residue 234 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 142 GLU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain d residue 276 ASN Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 176 MET Chi-restraints excluded: chain e residue 235 VAL Chi-restraints excluded: chain e residue 250 VAL Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 306 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 214 optimal weight: 0.1980 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 270 optimal weight: 4.9990 chunk 210 optimal weight: 0.2980 chunk 84 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 297 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 ASN f 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.101473 restraints weight = 52043.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.103809 restraints weight = 34052.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.105435 restraints weight = 25158.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106608 restraints weight = 20099.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.107458 restraints weight = 16917.351| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33828 Z= 0.132 Angle : 0.639 16.401 46104 Z= 0.299 Chirality : 0.044 0.155 5184 Planarity : 0.004 0.043 5988 Dihedral : 4.526 29.903 4614 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.55 % Allowed : 24.89 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.13), residues: 4224 helix: 0.78 (0.15), residues: 1248 sheet: -2.02 (0.26), residues: 384 loop : -1.41 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 284 TYR 0.022 0.001 TYR B 292 PHE 0.016 0.001 PHE a 348 TRP 0.019 0.001 TRP D 280 Details of bonding type rmsd covalent geometry : bond 0.00319 (33828) covalent geometry : angle 0.63855 (46104) hydrogen bonds : bond 0.03260 ( 896) hydrogen bonds : angle 4.04434 ( 2526) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 463 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 23 SER cc_start: 0.8295 (p) cc_final: 0.8048 (m) REVERT: B 271 MET cc_start: 0.9227 (tpt) cc_final: 0.8956 (tpt) REVERT: B 273 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: C 305 GLU cc_start: 0.7532 (pt0) cc_final: 0.7257 (tt0) REVERT: D 23 SER cc_start: 0.8555 (p) cc_final: 0.8309 (m) REVERT: E 23 SER cc_start: 0.8440 (p) cc_final: 0.8127 (m) REVERT: a 5 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8416 (p) REVERT: a 220 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8163 (mtm180) REVERT: a 260 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6161 (mm-30) REVERT: a 304 LYS cc_start: 0.8699 (pttm) cc_final: 0.8436 (pttm) REVERT: b 72 VAL cc_start: 0.9085 (p) cc_final: 0.8750 (t) REVERT: b 260 GLU cc_start: 0.6462 (mm-30) cc_final: 0.5140 (pt0) REVERT: b 281 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7243 (mt-10) REVERT: c 260 GLU cc_start: 0.6468 (mm-30) cc_final: 0.5772 (mm-30) REVERT: d 260 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6223 (mm-30) REVERT: d 306 GLU cc_start: 0.7449 (pp20) cc_final: 0.7246 (pp20) REVERT: e 72 VAL cc_start: 0.9095 (p) cc_final: 0.8771 (t) REVERT: e 235 VAL cc_start: 0.9579 (OUTLIER) cc_final: 0.9185 (t) REVERT: e 260 GLU cc_start: 0.6523 (mm-30) cc_final: 0.5313 (pt0) REVERT: f 5 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8192 (p) REVERT: f 235 VAL cc_start: 0.9573 (m) cc_final: 0.9176 (t) REVERT: f 260 GLU cc_start: 0.6449 (mm-30) cc_final: 0.5757 (mm-30) outliers start: 89 outliers final: 83 residues processed: 516 average time/residue: 0.1932 time to fit residues: 171.5229 Evaluate side-chains 536 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 448 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 99 ASP Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 203 GLU Chi-restraints excluded: chain a residue 220 ARG Chi-restraints excluded: chain a residue 228 PHE Chi-restraints excluded: chain a residue 235 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 228 PHE Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 203 GLU Chi-restraints excluded: chain c residue 215 GLU Chi-restraints excluded: chain c residue 234 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 176 MET Chi-restraints excluded: chain e residue 234 THR Chi-restraints excluded: chain e residue 235 VAL Chi-restraints excluded: chain e residue 250 VAL Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 306 GLU Chi-restraints excluded: chain f residue 350 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.0354 > 50: distance: 69 - 127: 35.242 distance: 83 - 114: 36.974 distance: 86 - 111: 32.060 distance: 99 - 104: 34.900 distance: 105 - 106: 57.425 distance: 105 - 108: 40.474 distance: 106 - 107: 39.892 distance: 106 - 111: 40.629 distance: 108 - 109: 40.139 distance: 108 - 110: 40.768 distance: 111 - 112: 3.088 distance: 112 - 113: 40.113 distance: 112 - 115: 40.770 distance: 113 - 120: 69.059 distance: 115 - 116: 30.986 distance: 116 - 117: 63.550 distance: 118 - 119: 23.951 distance: 120 - 121: 38.762 distance: 121 - 124: 57.733 distance: 122 - 127: 40.639 distance: 124 - 125: 40.613 distance: 124 - 126: 66.082 distance: 127 - 128: 53.940 distance: 129 - 131: 39.469 distance: 131 - 132: 41.254 distance: 132 - 135: 38.710 distance: 133 - 139: 57.751 distance: 135 - 136: 56.518 distance: 136 - 137: 33.875 distance: 136 - 138: 41.145 distance: 139 - 140: 40.646 distance: 140 - 143: 56.934 distance: 141 - 142: 39.131 distance: 141 - 144: 56.915 distance: 145 - 146: 56.618 distance: 146 - 147: 55.943 distance: 149 - 150: 41.099 distance: 150 - 151: 68.623 distance: 151 - 152: 39.797 distance: 151 - 156: 41.305 distance: 153 - 154: 40.524 distance: 153 - 155: 39.955 distance: 156 - 157: 40.804 distance: 157 - 158: 39.373 distance: 157 - 160: 39.047 distance: 158 - 159: 56.305 distance: 158 - 167: 39.029 distance: 160 - 161: 69.614 distance: 161 - 162: 38.670 distance: 163 - 164: 39.888 distance: 164 - 165: 69.179 distance: 164 - 166: 56.597 distance: 167 - 168: 39.586 distance: 167 - 173: 39.309 distance: 168 - 169: 57.927 distance: 168 - 171: 40.956 distance: 169 - 170: 55.468 distance: 169 - 174: 34.966 distance: 171 - 172: 40.694 distance: 172 - 173: 57.030