Starting phenix.real_space_refine on Thu Mar 5 06:22:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e84_31010/03_2026/7e84_31010.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e84_31010/03_2026/7e84_31010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e84_31010/03_2026/7e84_31010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e84_31010/03_2026/7e84_31010.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e84_31010/03_2026/7e84_31010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e84_31010/03_2026/7e84_31010.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 124 5.16 5 C 13228 2.51 5 N 3488 2.21 5 O 3740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20580 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3679 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 21, 'TRANS': 438} Chain breaks: 4 Chain: "B" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3679 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 21, 'TRANS': 438} Chain breaks: 4 Chain: "D" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3679 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 21, 'TRANS': 438} Chain breaks: 4 Chain: "G" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3679 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 21, 'TRANS': 438} Chain breaks: 4 Chain: "E" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "H" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "J" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "L" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Time building chain proxies: 4.67, per 1000 atoms: 0.23 Number of scatterers: 20580 At special positions: 0 Unit cell: (143.323, 143.323, 126.285, 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 124 16.00 O 3740 8.00 N 3488 7.00 C 13228 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: 1.62 Conformation dependent library (CDL) restraints added in 950.5 milliseconds 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4848 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 8 sheets defined 69.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 17 through 23 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.585A pdb=" N ARG A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.539A pdb=" N TYR A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.617A pdb=" N GLU A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 134 through 152 Processing helix chain 'A' and resid 166 through 177 removed outlier: 4.326A pdb=" N ARG A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 207 Processing helix chain 'A' and resid 227 through 249 removed outlier: 3.707A pdb=" N CYS A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 282 Proline residue: A 272 - end of helix removed outlier: 3.826A pdb=" N ASN A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 297 removed outlier: 4.006A pdb=" N VAL A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.772A pdb=" N ARG A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.848A pdb=" N ARG A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 346 Processing helix chain 'A' and resid 356 through 369 removed outlier: 4.227A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 3.607A pdb=" N ILE A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 450 removed outlier: 4.583A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.809A pdb=" N GLN A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 17 through 23 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.586A pdb=" N ARG B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.537A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.623A pdb=" N GLU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 134 through 152 Processing helix chain 'B' and resid 166 through 177 removed outlier: 4.371A pdb=" N ARG B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 207 Processing helix chain 'B' and resid 228 through 249 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 282 Proline residue: B 272 - end of helix removed outlier: 3.803A pdb=" N ASN B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 297 removed outlier: 4.074A pdb=" N VAL B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.774A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.779A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 346 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.130A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 removed outlier: 3.594A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 450 removed outlier: 4.586A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 489 removed outlier: 3.809A pdb=" N GLN B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 23 Proline residue: D 21 - end of helix Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.583A pdb=" N ARG D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.620A pdb=" N ILE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.620A pdb=" N GLU D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 133 Processing helix chain 'D' and resid 134 through 152 Processing helix chain 'D' and resid 166 through 177 removed outlier: 4.412A pdb=" N ARG D 170 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 207 Processing helix chain 'D' and resid 228 through 249 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 282 Proline residue: D 272 - end of helix removed outlier: 3.791A pdb=" N ASN D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 297 removed outlier: 4.002A pdb=" N VAL D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.783A pdb=" N ARG D 305 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.773A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 346 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.072A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 399 removed outlier: 3.617A pdb=" N ILE D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 386 " --> pdb=" O ALA D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 450 removed outlier: 4.591A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS D 421 " --> pdb=" O GLN D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 488 removed outlier: 3.808A pdb=" N GLN D 477 " --> pdb=" O SER D 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 16 Processing helix chain 'G' and resid 17 through 23 Proline residue: G 21 - end of helix Processing helix chain 'G' and resid 56 through 61 removed outlier: 3.581A pdb=" N ARG G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 91 through 101 removed outlier: 3.625A pdb=" N ILE G 95 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR G 99 " --> pdb=" O ILE G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 123 removed outlier: 3.621A pdb=" N GLU G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 133 Processing helix chain 'G' and resid 134 through 152 Processing helix chain 'G' and resid 166 through 177 removed outlier: 4.324A pdb=" N ARG G 170 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 207 Processing helix chain 'G' and resid 226 through 249 removed outlier: 3.702A pdb=" N PHE G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS G 231 " --> pdb=" O VAL G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 260 Processing helix chain 'G' and resid 260 through 282 Proline residue: G 272 - end of helix removed outlier: 3.814A pdb=" N ASN G 282 " --> pdb=" O VAL G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 296 Processing helix chain 'G' and resid 297 through 305 removed outlier: 3.788A pdb=" N ARG G 305 " --> pdb=" O LYS G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 320 removed outlier: 3.788A pdb=" N ARG G 311 " --> pdb=" O SER G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 346 Processing helix chain 'G' and resid 356 through 369 removed outlier: 4.050A pdb=" N TRP G 362 " --> pdb=" O PRO G 358 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR G 363 " --> pdb=" O ALA G 359 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR G 369 " --> pdb=" O ILE G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 399 removed outlier: 3.579A pdb=" N ILE G 385 " --> pdb=" O ILE G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 450 removed outlier: 4.592A pdb=" N VAL G 404 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP G 420 " --> pdb=" O ASN G 416 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS G 421 " --> pdb=" O GLN G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 473 through 488 removed outlier: 3.809A pdb=" N GLN G 477 " --> pdb=" O SER G 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 64 removed outlier: 3.800A pdb=" N GLU E 63 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.698A pdb=" N GLN E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 99 removed outlier: 3.748A pdb=" N TYR E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 103 removed outlier: 3.829A pdb=" N THR E 103 " --> pdb=" O THR E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 108 through 121 removed outlier: 3.872A pdb=" N THR E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 114 " --> pdb=" O ASP E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 169 through 180 Processing helix chain 'E' and resid 192 through 202 removed outlier: 3.507A pdb=" N GLN E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP E 202 " --> pdb=" O SER E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 210 removed outlier: 3.806A pdb=" N MET E 206 " --> pdb=" O ASP E 202 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN E 210 " --> pdb=" O MET E 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 64 removed outlier: 3.799A pdb=" N GLU H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.641A pdb=" N GLN H 76 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR H 78 " --> pdb=" O PHE H 74 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE H 81 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE H 82 " --> pdb=" O TYR H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.728A pdb=" N TYR H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 103 removed outlier: 3.841A pdb=" N THR H 103 " --> pdb=" O THR H 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 100 through 103' Processing helix chain 'H' and resid 108 through 121 removed outlier: 3.692A pdb=" N THR H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA H 114 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 147 through 157 Processing helix chain 'H' and resid 169 through 180 Processing helix chain 'H' and resid 192 through 202 Processing helix chain 'H' and resid 202 through 210 removed outlier: 3.776A pdb=" N MET H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN H 210 " --> pdb=" O MET H 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 64 removed outlier: 3.728A pdb=" N GLU J 63 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.698A pdb=" N GLN J 76 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE J 77 " --> pdb=" O THR J 73 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR J 78 " --> pdb=" O PHE J 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN J 80 " --> pdb=" O GLN J 76 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE J 81 " --> pdb=" O ILE J 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE J 82 " --> pdb=" O TYR J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 99 removed outlier: 3.722A pdb=" N TYR J 93 " --> pdb=" O THR J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 103 removed outlier: 3.827A pdb=" N THR J 103 " --> pdb=" O THR J 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 100 through 103' Processing helix chain 'J' and resid 108 through 121 removed outlier: 3.808A pdb=" N THR J 113 " --> pdb=" O GLU J 109 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA J 114 " --> pdb=" O ASP J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 135 Processing helix chain 'J' and resid 147 through 157 Processing helix chain 'J' and resid 169 through 180 Processing helix chain 'J' and resid 192 through 202 removed outlier: 3.625A pdb=" N ASP J 202 " --> pdb=" O SER J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 210 removed outlier: 3.811A pdb=" N MET J 206 " --> pdb=" O ASP J 202 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN J 210 " --> pdb=" O MET J 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 64 removed outlier: 3.732A pdb=" N GLU L 63 " --> pdb=" O GLY L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 82 removed outlier: 3.667A pdb=" N GLN L 76 " --> pdb=" O ASP L 72 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE L 77 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR L 78 " --> pdb=" O PHE L 74 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN L 80 " --> pdb=" O GLN L 76 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE L 81 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE L 82 " --> pdb=" O TYR L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 99 removed outlier: 3.749A pdb=" N TYR L 93 " --> pdb=" O THR L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 103 removed outlier: 3.837A pdb=" N THR L 103 " --> pdb=" O THR L 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 100 through 103' Processing helix chain 'L' and resid 108 through 121 removed outlier: 3.823A pdb=" N THR L 113 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA L 114 " --> pdb=" O ASP L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 135 Processing helix chain 'L' and resid 147 through 157 Processing helix chain 'L' and resid 169 through 180 Processing helix chain 'L' and resid 192 through 202 removed outlier: 3.507A pdb=" N GLN L 200 " --> pdb=" O LEU L 196 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP L 202 " --> pdb=" O SER L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 210 removed outlier: 3.887A pdb=" N MET L 206 " --> pdb=" O ASP L 202 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN L 210 " --> pdb=" O MET L 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.812A pdb=" N THR A 50 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N TYR A 83 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 44 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE A 85 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A 46 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.812A pdb=" N THR B 50 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N TYR B 83 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 44 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE B 85 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN B 46 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 50 through 55 removed outlier: 3.813A pdb=" N THR D 50 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N TYR D 83 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL D 44 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE D 85 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN D 46 " --> pdb=" O PHE D 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 50 through 55 removed outlier: 3.808A pdb=" N THR G 50 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N TYR G 83 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 44 " --> pdb=" O TYR G 83 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE G 85 " --> pdb=" O VAL G 44 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN G 46 " --> pdb=" O PHE G 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 68 through 70 Processing sheet with id=AA6, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AA7, first strand: chain 'J' and resid 68 through 70 Processing sheet with id=AA8, first strand: chain 'L' and resid 68 through 70 1176 hydrogen bonds defined for protein. 3417 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: 3.16 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6616 1.34 - 1.46: 5127 1.46 - 1.58: 9137 1.58 - 1.70: 0 1.70 - 1.81: 200 Bond restraints: 21080 Sorted by residual: bond pdb=" CB MET A 27 " pdb=" CG MET A 27 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CB MET D 27 " pdb=" CG MET D 27 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CB GLU G 346 " pdb=" CG GLU G 346 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.99e-01 bond pdb=" CA ASP E 86 " pdb=" CB ASP E 86 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.82e-02 3.02e+03 8.75e-01 bond pdb=" CB GLU B 346 " pdb=" CG GLU B 346 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.75e-01 ... (remaining 21075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 28302 2.55 - 5.10: 184 5.10 - 7.65: 22 7.65 - 10.20: 0 10.20 - 12.76: 4 Bond angle restraints: 28512 Sorted by residual: angle pdb=" N ILE D 91 " pdb=" CA ILE D 91 " pdb=" C ILE D 91 " ideal model delta sigma weight residual 112.96 108.11 4.85 1.00e+00 1.00e+00 2.36e+01 angle pdb=" N ILE B 91 " pdb=" CA ILE B 91 " pdb=" C ILE B 91 " ideal model delta sigma weight residual 113.42 108.04 5.38 1.17e+00 7.31e-01 2.11e+01 angle pdb=" N ILE A 91 " pdb=" CA ILE A 91 " pdb=" C ILE A 91 " ideal model delta sigma weight residual 113.42 108.10 5.32 1.17e+00 7.31e-01 2.07e+01 angle pdb=" CB MET A 27 " pdb=" CG MET A 27 " pdb=" SD MET A 27 " ideal model delta sigma weight residual 112.70 125.46 -12.76 3.00e+00 1.11e-01 1.81e+01 angle pdb=" CB MET D 27 " pdb=" CG MET D 27 " pdb=" SD MET D 27 " ideal model delta sigma weight residual 112.70 125.26 -12.56 3.00e+00 1.11e-01 1.75e+01 ... (remaining 28507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11164 17.84 - 35.68: 1079 35.68 - 53.51: 217 53.51 - 71.35: 34 71.35 - 89.19: 14 Dihedral angle restraints: 12508 sinusoidal: 5020 harmonic: 7488 Sorted by residual: dihedral pdb=" CB GLU G 136 " pdb=" CG GLU G 136 " pdb=" CD GLU G 136 " pdb=" OE1 GLU G 136 " ideal model delta sinusoidal sigma weight residual 0.00 89.19 -89.19 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA HIS G 77 " pdb=" C HIS G 77 " pdb=" N PRO G 78 " pdb=" CA PRO G 78 " ideal model delta harmonic sigma weight residual -180.00 -164.10 -15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA SER A 69 " pdb=" C SER A 69 " pdb=" N SER A 70 " pdb=" CA SER A 70 " ideal model delta harmonic sigma weight residual 180.00 164.11 15.89 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 12505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2005 0.029 - 0.058: 677 0.058 - 0.087: 323 0.087 - 0.115: 102 0.115 - 0.144: 13 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA THR L 170 " pdb=" N THR L 170 " pdb=" C THR L 170 " pdb=" CB THR L 170 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA THR J 170 " pdb=" N THR J 170 " pdb=" C THR J 170 " pdb=" CB THR J 170 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA THR H 170 " pdb=" N THR H 170 " pdb=" C THR H 170 " pdb=" CB THR H 170 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 3117 not shown) Planarity restraints: 3644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 207 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO G 208 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 208 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 208 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 207 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO B 208 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 27 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C MET D 27 " 0.031 2.00e-02 2.50e+03 pdb=" O MET D 27 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO D 28 " -0.011 2.00e-02 2.50e+03 ... (remaining 3641 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5068 2.79 - 3.32: 20373 3.32 - 3.85: 33296 3.85 - 4.37: 39567 4.37 - 4.90: 67330 Nonbonded interactions: 165634 Sorted by model distance: nonbonded pdb=" OG1 THR D 65 " pdb=" OH TYR D 99 " model vdw 2.263 3.040 nonbonded pdb=" OE2 GLU B 71 " pdb=" OH TYR H 57 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR G 65 " pdb=" OH TYR G 99 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR A 65 " pdb=" OH TYR A 99 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" OH TYR B 99 " model vdw 2.266 3.040 ... (remaining 165629 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.940 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 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 : 0.002 0.031 21080 Z= 0.099 Angle : 0.534 12.756 28512 Z= 0.275 Chirality : 0.038 0.144 3120 Planarity : 0.003 0.053 3644 Dihedral : 14.852 89.189 7660 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.02 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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 are not related in a simple way. whole: -0.03 (0.17), residues: 2492 helix: 1.07 (0.13), residues: 1612 sheet: -2.41 (0.53), residues: 40 loop : -2.09 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 207 TYR 0.009 0.001 TYR G 188 PHE 0.016 0.001 PHE D 493 TRP 0.009 0.001 TRP D 362 HIS 0.003 0.000 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00211 (21080) covalent geometry : angle 0.53395 (28512) hydrogen bonds : bond 0.21595 ( 1176) hydrogen bonds : angle 6.36574 ( 3417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.863 Fit side-chains REVERT: A 27 MET cc_start: 0.2190 (tmm) cc_final: 0.1009 (pmm) REVERT: A 46 ASN cc_start: 0.8649 (t0) cc_final: 0.8192 (t0) REVERT: B 27 MET cc_start: 0.1926 (tmm) cc_final: 0.0800 (pmm) REVERT: B 46 ASN cc_start: 0.8659 (t0) cc_final: 0.8213 (t0) REVERT: B 429 ARG cc_start: 0.6940 (ttm-80) cc_final: 0.6602 (mmt90) REVERT: D 27 MET cc_start: 0.1941 (tmm) cc_final: 0.0816 (pmm) REVERT: D 46 ASN cc_start: 0.8650 (t0) cc_final: 0.8205 (t0) REVERT: D 429 ARG cc_start: 0.6987 (ttm-80) cc_final: 0.6632 (mmt90) REVERT: G 27 MET cc_start: 0.1967 (tmm) cc_final: 0.0811 (pmm) REVERT: G 46 ASN cc_start: 0.8647 (t0) cc_final: 0.8197 (t0) REVERT: G 429 ARG cc_start: 0.6928 (ttm-80) cc_final: 0.6532 (mmt90) REVERT: E 168 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6572 (tm-30) REVERT: J 168 GLU cc_start: 0.6822 (tm-30) cc_final: 0.6608 (tm-30) REVERT: L 148 MET cc_start: 0.5826 (tpp) cc_final: 0.5605 (tpt) REVERT: L 168 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6602 (tm-30) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.1640 time to fit residues: 94.8942 Evaluate side-chains 302 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS A 416 ASN B 414 HIS D 414 HIS D 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.214761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.197342 restraints weight = 22327.507| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 0.72 r_work: 0.3891 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3852 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work: 0.3803 rms_B_bonded: 2.48 restraints_weight: 0.1250 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21080 Z= 0.146 Angle : 0.563 7.296 28512 Z= 0.299 Chirality : 0.041 0.166 3120 Planarity : 0.004 0.053 3644 Dihedral : 3.960 14.811 2804 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.78 % Favored : 93.06 % Rotamer: Outliers : 0.54 % Allowed : 7.96 % Favored : 91.50 % 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 are not related in a simple way. whole: 0.42 (0.17), residues: 2492 helix: 1.44 (0.13), residues: 1600 sheet: -1.49 (0.67), residues: 40 loop : -1.97 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 142 TYR 0.011 0.001 TYR D 188 PHE 0.020 0.002 PHE E 178 TRP 0.009 0.001 TRP A 362 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00321 (21080) covalent geometry : angle 0.56311 (28512) hydrogen bonds : bond 0.04907 ( 1176) hydrogen bonds : angle 4.53046 ( 3417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 303 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 204 VAL cc_start: 0.7563 (m) cc_final: 0.7322 (t) REVERT: A 475 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: B 429 ARG cc_start: 0.7084 (ttm-80) cc_final: 0.6733 (mmt180) REVERT: B 475 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: D 429 ARG cc_start: 0.7093 (ttm-80) cc_final: 0.6731 (mmt180) REVERT: D 475 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: G 204 VAL cc_start: 0.7441 (m) cc_final: 0.7216 (t) REVERT: G 429 ARG cc_start: 0.7012 (ttm-80) cc_final: 0.6688 (mmt180) REVERT: G 475 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7663 (mt-10) outliers start: 12 outliers final: 4 residues processed: 311 average time/residue: 0.1638 time to fit residues: 75.9009 Evaluate side-chains 284 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 276 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 249 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 0.0770 chunk 142 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 224 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS A 416 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.214076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.196913 restraints weight = 22405.398| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 0.73 r_work: 0.3870 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work: 0.3768 rms_B_bonded: 2.55 restraints_weight: 0.1250 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21080 Z= 0.137 Angle : 0.531 6.802 28512 Z= 0.280 Chirality : 0.040 0.189 3120 Planarity : 0.004 0.052 3644 Dihedral : 3.971 15.667 2804 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.06 % Favored : 92.78 % Rotamer: Outliers : 0.50 % Allowed : 11.26 % Favored : 88.25 % 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 are not related in a simple way. whole: 0.59 (0.17), residues: 2492 helix: 1.59 (0.13), residues: 1600 sheet: -1.34 (0.68), residues: 40 loop : -1.95 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 296 TYR 0.012 0.001 TYR G 188 PHE 0.022 0.002 PHE E 131 TRP 0.008 0.001 TRP A 362 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00307 (21080) covalent geometry : angle 0.53067 (28512) hydrogen bonds : bond 0.04270 ( 1176) hydrogen bonds : angle 4.27023 ( 3417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 274 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: B 429 ARG cc_start: 0.7084 (ttm-80) cc_final: 0.6804 (mmt180) REVERT: B 475 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: D 429 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.6791 (mmt180) REVERT: D 475 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: G 429 ARG cc_start: 0.7088 (ttm-80) cc_final: 0.6800 (mmt180) REVERT: G 475 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7708 (mt-10) outliers start: 11 outliers final: 5 residues processed: 282 average time/residue: 0.1533 time to fit residues: 64.6654 Evaluate side-chains 274 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 265 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 135 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 140 optimal weight: 0.0030 chunk 64 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 chunk 245 optimal weight: 0.1980 chunk 250 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.215439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.193084 restraints weight = 22471.081| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 0.94 r_work: 0.3846 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.3652 rms_B_bonded: 4.99 restraints_weight: 0.1250 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21080 Z= 0.115 Angle : 0.512 8.437 28512 Z= 0.268 Chirality : 0.039 0.203 3120 Planarity : 0.004 0.051 3644 Dihedral : 3.912 16.075 2804 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.74 % Favored : 93.10 % Rotamer: Outliers : 1.13 % Allowed : 11.26 % Favored : 87.61 % 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 are not related in a simple way. whole: 0.74 (0.17), residues: 2492 helix: 1.76 (0.13), residues: 1596 sheet: -1.59 (0.66), residues: 40 loop : -1.96 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 51 TYR 0.012 0.001 TYR D 188 PHE 0.024 0.001 PHE H 131 TRP 0.008 0.001 TRP A 362 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00249 (21080) covalent geometry : angle 0.51226 (28512) hydrogen bonds : bond 0.03748 ( 1176) hydrogen bonds : angle 4.11742 ( 3417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 275 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: B 27 MET cc_start: 0.2041 (tmm) cc_final: 0.1427 (tmm) REVERT: B 429 ARG cc_start: 0.7280 (ttm-80) cc_final: 0.7037 (mmt180) REVERT: B 475 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: D 429 ARG cc_start: 0.7295 (ttm-80) cc_final: 0.7039 (mmt180) REVERT: D 475 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: G 429 ARG cc_start: 0.7261 (ttm-80) cc_final: 0.7004 (mmt180) REVERT: G 475 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: E 179 PHE cc_start: 0.7708 (m-10) cc_final: 0.7491 (m-10) REVERT: H 106 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8360 (p) REVERT: L 148 MET cc_start: 0.7913 (tpp) cc_final: 0.7596 (tpt) outliers start: 25 outliers final: 5 residues processed: 291 average time/residue: 0.1445 time to fit residues: 64.8085 Evaluate side-chains 273 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 263 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 140 optimal weight: 0.3980 chunk 207 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 20 optimal weight: 0.0670 chunk 41 optimal weight: 10.0000 chunk 16 optimal weight: 0.0770 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 416 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 HIS ** G 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN G 77 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.218563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.202399 restraints weight = 22238.167| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 0.80 r_work: 0.3889 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 1.75 restraints_weight: 0.2500 r_work: 0.3752 rms_B_bonded: 3.61 restraints_weight: 0.1250 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21080 Z= 0.106 Angle : 0.509 9.379 28512 Z= 0.264 Chirality : 0.038 0.220 3120 Planarity : 0.004 0.050 3644 Dihedral : 3.852 16.482 2804 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.70 % Favored : 93.14 % Rotamer: Outliers : 1.04 % Allowed : 12.21 % Favored : 86.75 % 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 are not related in a simple way. whole: 0.83 (0.17), residues: 2492 helix: 1.83 (0.13), residues: 1600 sheet: -1.22 (0.71), residues: 40 loop : -1.96 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 51 TYR 0.011 0.001 TYR G 188 PHE 0.025 0.001 PHE J 178 TRP 0.006 0.001 TRP A 362 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00223 (21080) covalent geometry : angle 0.50903 (28512) hydrogen bonds : bond 0.03544 ( 1176) hydrogen bonds : angle 4.01334 ( 3417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 269 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: B 27 MET cc_start: 0.2043 (tmm) cc_final: 0.1832 (tmm) REVERT: B 429 ARG cc_start: 0.7331 (ttm-80) cc_final: 0.7009 (mmt180) REVERT: B 475 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: D 429 ARG cc_start: 0.7321 (ttm-80) cc_final: 0.6991 (mmt180) REVERT: D 475 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: G 429 ARG cc_start: 0.7384 (ttm-80) cc_final: 0.7055 (mmt180) REVERT: G 475 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: H 106 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8331 (p) REVERT: L 148 MET cc_start: 0.7754 (tpp) cc_final: 0.7368 (tpt) outliers start: 23 outliers final: 12 residues processed: 283 average time/residue: 0.1379 time to fit residues: 60.4877 Evaluate side-chains 281 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 264 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 77 HIS Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain J residue 213 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 211 optimal weight: 5.9990 chunk 210 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS A 414 HIS ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 HIS ** G 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.216293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.193585 restraints weight = 22103.300| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 0.91 r_work: 0.3863 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21080 Z= 0.114 Angle : 0.517 9.848 28512 Z= 0.265 Chirality : 0.039 0.137 3120 Planarity : 0.004 0.049 3644 Dihedral : 3.858 16.163 2804 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.78 % Favored : 93.06 % Rotamer: Outliers : 1.13 % Allowed : 12.79 % Favored : 86.08 % 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 are not related in a simple way. whole: 0.89 (0.17), residues: 2492 helix: 1.85 (0.13), residues: 1620 sheet: -1.22 (0.65), residues: 40 loop : -1.99 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 51 TYR 0.011 0.001 TYR G 188 PHE 0.029 0.001 PHE J 178 TRP 0.007 0.001 TRP A 362 HIS 0.003 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00250 (21080) covalent geometry : angle 0.51717 (28512) hydrogen bonds : bond 0.03508 ( 1176) hydrogen bonds : angle 3.98493 ( 3417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 269 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7665 (mt-10) REVERT: B 90 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7169 (m-30) REVERT: B 429 ARG cc_start: 0.7366 (ttm-80) cc_final: 0.7044 (mmt180) REVERT: B 475 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: D 429 ARG cc_start: 0.7314 (ttm-80) cc_final: 0.6990 (mmt180) REVERT: D 475 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: G 429 ARG cc_start: 0.7341 (ttm-80) cc_final: 0.7048 (mmt180) REVERT: G 475 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: L 148 MET cc_start: 0.7693 (tpp) cc_final: 0.7355 (tpt) outliers start: 25 outliers final: 14 residues processed: 283 average time/residue: 0.1379 time to fit residues: 60.1131 Evaluate side-chains 284 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 265 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain L residue 64 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 229 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 152 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 414 HIS ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 HIS ** G 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.214225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.197160 restraints weight = 22186.582| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 0.72 r_work: 0.3848 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work: 0.3753 rms_B_bonded: 2.50 restraints_weight: 0.1250 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21080 Z= 0.143 Angle : 0.560 15.629 28512 Z= 0.286 Chirality : 0.040 0.245 3120 Planarity : 0.004 0.048 3644 Dihedral : 3.958 15.779 2804 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.02 % Favored : 92.82 % Rotamer: Outliers : 1.22 % Allowed : 13.29 % Favored : 85.49 % 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 are not related in a simple way. whole: 0.82 (0.17), residues: 2492 helix: 1.79 (0.13), residues: 1624 sheet: -1.48 (0.57), residues: 40 loop : -2.00 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 51 TYR 0.013 0.001 TYR G 188 PHE 0.038 0.002 PHE L 178 TRP 0.007 0.001 TRP A 362 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00332 (21080) covalent geometry : angle 0.56019 (28512) hydrogen bonds : bond 0.03727 ( 1176) hydrogen bonds : angle 3.99642 ( 3417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: B 90 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: B 429 ARG cc_start: 0.7330 (ttm-80) cc_final: 0.6938 (mmt180) REVERT: B 475 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: D 429 ARG cc_start: 0.7333 (ttm-80) cc_final: 0.6936 (mmt180) REVERT: D 475 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: G 429 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.7080 (mmt180) REVERT: G 475 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: L 148 MET cc_start: 0.7843 (tpp) cc_final: 0.7559 (tmm) outliers start: 27 outliers final: 10 residues processed: 287 average time/residue: 0.1344 time to fit residues: 60.4796 Evaluate side-chains 280 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 265 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 213 GLN Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 213 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.1980 chunk 160 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 HIS ** G 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.217094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.200646 restraints weight = 22197.392| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 0.81 r_work: 0.3869 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.3738 rms_B_bonded: 3.43 restraints_weight: 0.1250 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21080 Z= 0.109 Angle : 0.518 10.285 28512 Z= 0.267 Chirality : 0.039 0.199 3120 Planarity : 0.004 0.048 3644 Dihedral : 3.886 16.640 2804 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.82 % Favored : 93.02 % Rotamer: Outliers : 1.18 % Allowed : 13.61 % Favored : 85.22 % 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 are not related in a simple way. whole: 0.88 (0.17), residues: 2492 helix: 1.85 (0.13), residues: 1624 sheet: -1.27 (0.62), residues: 40 loop : -2.02 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 51 TYR 0.012 0.001 TYR G 188 PHE 0.037 0.002 PHE H 178 TRP 0.008 0.001 TRP G 362 HIS 0.003 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00237 (21080) covalent geometry : angle 0.51849 (28512) hydrogen bonds : bond 0.03391 ( 1176) hydrogen bonds : angle 3.92357 ( 3417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 475 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: B 90 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: B 429 ARG cc_start: 0.7331 (ttm-80) cc_final: 0.6954 (mmt180) REVERT: B 475 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: D 429 ARG cc_start: 0.7348 (ttm-80) cc_final: 0.6967 (mmt180) REVERT: D 475 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: G 90 ASP cc_start: 0.7851 (m-30) cc_final: 0.7610 (m-30) REVERT: G 429 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.7158 (mmt180) REVERT: G 475 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: H 208 SER cc_start: 0.8560 (m) cc_final: 0.8240 (m) REVERT: L 148 MET cc_start: 0.7801 (tpp) cc_final: 0.7506 (tmm) outliers start: 26 outliers final: 15 residues processed: 288 average time/residue: 0.1330 time to fit residues: 59.1771 Evaluate side-chains 285 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 265 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 77 HIS Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 213 GLN Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 213 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.207173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.189719 restraints weight = 22214.640| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 0.69 r_work: 0.3743 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work: 0.3605 rms_B_bonded: 2.87 restraints_weight: 0.1250 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 21080 Z= 0.330 Angle : 0.745 14.204 28512 Z= 0.377 Chirality : 0.048 0.179 3120 Planarity : 0.006 0.053 3644 Dihedral : 4.566 17.802 2804 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.78 % Favored : 92.05 % Rotamer: Outliers : 0.63 % Allowed : 14.06 % Favored : 85.31 % 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 are not related in a simple way. whole: 0.27 (0.17), residues: 2492 helix: 1.31 (0.13), residues: 1620 sheet: -0.92 (0.68), residues: 40 loop : -2.10 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 51 TYR 0.018 0.002 TYR G 188 PHE 0.039 0.003 PHE H 178 TRP 0.010 0.002 TRP D 362 HIS 0.006 0.002 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00800 (21080) covalent geometry : angle 0.74502 (28512) hydrogen bonds : bond 0.04956 ( 1176) hydrogen bonds : angle 4.35837 ( 3417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 289 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: B 90 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: B 429 ARG cc_start: 0.7279 (ttm-80) cc_final: 0.6959 (mmt180) REVERT: B 475 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7918 (mt-10) REVERT: D 429 ARG cc_start: 0.7285 (ttm-80) cc_final: 0.6949 (mmt180) REVERT: D 475 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: G 429 ARG cc_start: 0.7358 (ttm-80) cc_final: 0.6972 (mmt180) REVERT: G 475 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: L 148 MET cc_start: 0.8012 (tpp) cc_final: 0.7793 (mmm) outliers start: 14 outliers final: 7 residues processed: 300 average time/residue: 0.1522 time to fit residues: 69.4755 Evaluate side-chains 284 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 272 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain L residue 64 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 158 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 416 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 HIS ** G 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.209975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.188126 restraints weight = 22359.281| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 0.93 r_work: 0.3795 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work: 0.3629 rms_B_bonded: 4.28 restraints_weight: 0.1250 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21080 Z= 0.166 Angle : 0.611 12.897 28512 Z= 0.315 Chirality : 0.042 0.194 3120 Planarity : 0.004 0.058 3644 Dihedral : 4.339 18.305 2804 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.98 % Favored : 92.86 % Rotamer: Outliers : 0.77 % Allowed : 14.87 % Favored : 84.36 % 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 are not related in a simple way. whole: 0.47 (0.17), residues: 2492 helix: 1.56 (0.13), residues: 1612 sheet: -0.83 (0.71), residues: 40 loop : -2.22 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 51 TYR 0.015 0.001 TYR G 188 PHE 0.037 0.002 PHE H 178 TRP 0.010 0.001 TRP B 362 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00390 (21080) covalent geometry : angle 0.61135 (28512) hydrogen bonds : bond 0.04020 ( 1176) hydrogen bonds : angle 4.14300 ( 3417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 271 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 86 ASP cc_start: 0.7933 (p0) cc_final: 0.7721 (p0) REVERT: A 204 VAL cc_start: 0.7901 (m) cc_final: 0.7700 (t) REVERT: A 475 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: B 90 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: B 204 VAL cc_start: 0.7781 (m) cc_final: 0.7563 (t) REVERT: B 429 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.7103 (mmt180) REVERT: B 475 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: D 204 VAL cc_start: 0.7744 (m) cc_final: 0.7515 (t) REVERT: D 429 ARG cc_start: 0.7375 (ttm-80) cc_final: 0.7094 (mmt180) REVERT: D 475 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7928 (mt-10) REVERT: G 429 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7148 (mmt180) REVERT: G 475 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7936 (mt-10) outliers start: 17 outliers final: 7 residues processed: 281 average time/residue: 0.1518 time to fit residues: 64.1028 Evaluate side-chains 279 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 267 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain L residue 64 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 2 optimal weight: 0.2980 chunk 141 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 HIS ** G 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.214873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.197468 restraints weight = 22313.894| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 0.72 r_work: 0.3832 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work: 0.3706 rms_B_bonded: 2.99 restraints_weight: 0.1250 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21080 Z= 0.119 Angle : 0.567 13.804 28512 Z= 0.289 Chirality : 0.040 0.177 3120 Planarity : 0.004 0.052 3644 Dihedral : 4.051 16.983 2804 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.98 % Favored : 92.86 % Rotamer: Outliers : 0.99 % Allowed : 14.65 % Favored : 84.36 % 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 are not related in a simple way. whole: 0.70 (0.17), residues: 2492 helix: 1.74 (0.13), residues: 1612 sheet: -1.26 (0.63), residues: 40 loop : -2.11 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 51 TYR 0.012 0.001 TYR D 188 PHE 0.033 0.002 PHE H 178 TRP 0.009 0.001 TRP B 362 HIS 0.005 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00260 (21080) covalent geometry : angle 0.56714 (28512) hydrogen bonds : bond 0.03499 ( 1176) hydrogen bonds : angle 3.98292 ( 3417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5407.93 seconds wall clock time: 93 minutes 7.76 seconds (5587.76 seconds total)