Starting phenix.real_space_refine on Thu Mar 5 06:44:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f3f_31433/03_2026/7f3f_31433.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f3f_31433/03_2026/7f3f_31433.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/7f3f_31433/03_2026/7f3f_31433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f3f_31433/03_2026/7f3f_31433.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f3f_31433/03_2026/7f3f_31433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f3f_31433/03_2026/7f3f_31433.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 17 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: 4.80, 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 1.0 seconds 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: 125 helices and 8 sheets defined 69.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 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: 3.579A 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 91 through 101 removed outlier: 3.574A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.672A 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: 4.265A pdb=" N ARG A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.126A 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: 3.616A 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: 3.754A pdb=" N ASN A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 297 removed outlier: 4.021A pdb=" N VAL A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.714A pdb=" N ARG A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.768A 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: 4.126A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 removed outlier: 3.659A pdb=" N ILE A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 450 removed outlier: 4.605A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.936A pdb=" N GLN A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.958A 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: 3.579A 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 91 through 101 removed outlier: 3.570A pdb=" N ILE B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.679A 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: 4.290A pdb=" N ARG B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.117A 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: 3.738A pdb=" N ASN B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.739A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.764A 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: 4.094A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.660A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 450 removed outlier: 4.607A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 489 removed outlier: 3.937A pdb=" N GLN B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 3.825A 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: 3.580A 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: 3.574A pdb=" N ILE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.675A 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: 4.293A pdb=" N ARG D 170 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 4.119A 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 227 through 249 removed outlier: 3.968A pdb=" N CYS D 231 " --> pdb=" O VAL D 227 " (cutoff:3.500A) 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: 3.737A pdb=" N ASN D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 297 removed outlier: 3.996A pdb=" N VAL D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.545A pdb=" N PHE D 301 " --> pdb=" O PHE D 298 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 305 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.776A 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: 4.126A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 removed outlier: 3.653A pdb=" N ILE D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 386 " --> pdb=" O ALA D 382 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 450 removed outlier: 4.600A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS D 421 " --> pdb=" O GLN D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 488 removed outlier: 3.938A 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: 3.573A 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: 3.571A pdb=" N ILE G 95 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR G 99 " --> pdb=" O ILE G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 123 removed outlier: 3.674A pdb=" N GLU G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 133 removed outlier: 3.506A pdb=" N CYS G 133 " --> pdb=" O GLY G 130 " (cutoff:3.500A) No H-bonds generated for '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: 4.267A pdb=" N ARG G 170 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 4.099A 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 227 through 249 removed outlier: 3.652A 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: 3.742A pdb=" N ASN G 282 " --> pdb=" O VAL G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 297 removed outlier: 4.056A pdb=" N VAL G 297 " --> pdb=" O ARG G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 305 removed outlier: 3.732A pdb=" N ARG G 305 " --> pdb=" O LYS G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 320 removed outlier: 3.812A 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: 4.150A pdb=" N TRP G 362 " --> pdb=" O PRO G 358 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR G 363 " --> pdb=" O ALA G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 400 removed outlier: 3.644A pdb=" N ILE G 385 " --> pdb=" O ILE G 381 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE G 386 " --> pdb=" O ALA G 382 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G 400 " --> pdb=" O LEU G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 417 removed outlier: 4.609A pdb=" N VAL G 404 " --> pdb=" O LEU G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 450 Processing helix chain 'G' and resid 473 through 489 removed outlier: 3.936A pdb=" N GLN G 477 " --> pdb=" O SER G 473 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR G 489 " --> pdb=" O LEU G 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 64 removed outlier: 3.668A pdb=" N GLU E 63 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.829A pdb=" N GLN E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 99 removed outlier: 3.749A pdb=" N TYR E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 103 removed outlier: 3.756A 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: 3.792A pdb=" N THR E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 3.590A 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 Processing helix chain 'E' and resid 202 through 210 removed outlier: 3.660A pdb=" N MET E 206 " --> pdb=" O ASP E 202 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN E 210 " --> pdb=" O MET E 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 64 removed outlier: 3.667A pdb=" N GLU H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.826A pdb=" N GLN H 76 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR H 78 " --> pdb=" O PHE H 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE H 81 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE H 82 " --> pdb=" O TYR H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.749A pdb=" N TYR H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 103 removed outlier: 3.756A 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: 3.822A pdb=" N THR H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.700A pdb=" N MET H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN H 210 " --> pdb=" O MET H 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 64 removed outlier: 3.667A pdb=" N GLU J 63 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.826A pdb=" N GLN J 76 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE J 77 " --> pdb=" O THR J 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR J 78 " --> pdb=" O PHE J 74 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE J 81 " --> pdb=" O ILE J 77 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE J 82 " --> pdb=" O TYR J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 99 removed outlier: 3.749A pdb=" N TYR J 93 " --> pdb=" O THR J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 103 removed outlier: 3.756A 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: 3.822A pdb=" N THR J 113 " --> pdb=" O GLU J 109 " (cutoff:3.500A) removed outlier: 3.595A 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 Processing helix chain 'J' and resid 202 through 210 removed outlier: 3.637A pdb=" N MET J 206 " --> pdb=" O ASP J 202 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN J 210 " --> pdb=" O MET J 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 64 removed outlier: 3.681A pdb=" N GLU L 63 " --> pdb=" O GLY L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 82 removed outlier: 3.828A pdb=" N GLN L 76 " --> pdb=" O ASP L 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE L 77 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR L 78 " --> pdb=" O PHE L 74 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE L 81 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.786A 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: 3.759A 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: 3.793A pdb=" N THR L 113 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 3.590A 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 Processing helix chain 'L' and resid 202 through 210 removed outlier: 3.661A pdb=" N MET L 206 " --> pdb=" O ASP L 202 " (cutoff:3.500A) removed outlier: 3.710A 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: 3.523A pdb=" N GLN A 82 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.810A pdb=" N THR B 50 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 82 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 50 through 55 removed outlier: 3.812A pdb=" N THR D 50 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 82 " --> pdb=" O HIS D 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 50 through 55 removed outlier: 3.812A pdb=" N THR G 50 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN G 82 " --> pdb=" O HIS G 77 " (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 1185 hydrogen bonds defined for protein. 3462 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: 3.13 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3919 1.33 - 1.45: 5510 1.45 - 1.57: 11451 1.57 - 1.70: 0 1.70 - 1.82: 200 Bond restraints: 21080 Sorted by residual: bond pdb=" C ARG G 418 " pdb=" O ARG G 418 " ideal model delta sigma weight residual 1.234 1.205 0.029 1.17e-02 7.31e+03 6.14e+00 bond pdb=" C GLN A 417 " pdb=" O GLN A 417 " ideal model delta sigma weight residual 1.236 1.208 0.029 1.22e-02 6.72e+03 5.47e+00 bond pdb=" C GLN D 417 " pdb=" O GLN D 417 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.28e-02 6.10e+03 5.15e+00 bond pdb=" C ASN A 416 " pdb=" O ASN A 416 " ideal model delta sigma weight residual 1.236 1.208 0.028 1.32e-02 5.74e+03 4.36e+00 bond pdb=" C ASN D 416 " pdb=" O ASN D 416 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.32e-02 5.74e+03 4.08e+00 ... (remaining 21075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 28206 2.51 - 5.02: 252 5.02 - 7.53: 38 7.53 - 10.05: 8 10.05 - 12.56: 8 Bond angle restraints: 28512 Sorted by residual: angle pdb=" N GLN B 417 " pdb=" CA GLN B 417 " pdb=" C GLN B 417 " ideal model delta sigma weight residual 113.12 104.25 8.87 1.25e+00 6.40e-01 5.03e+01 angle pdb=" N GLN G 417 " pdb=" CA GLN G 417 " pdb=" C GLN G 417 " ideal model delta sigma weight residual 113.38 105.52 7.86 1.23e+00 6.61e-01 4.08e+01 angle pdb=" N GLN A 417 " pdb=" CA GLN A 417 " pdb=" C GLN A 417 " ideal model delta sigma weight residual 111.69 104.26 7.43 1.23e+00 6.61e-01 3.65e+01 angle pdb=" N GLN D 417 " pdb=" CA GLN D 417 " pdb=" C GLN D 417 " ideal model delta sigma weight residual 112.45 104.47 7.98 1.39e+00 5.18e-01 3.30e+01 angle pdb=" CB ARG D 418 " pdb=" CG ARG D 418 " pdb=" CD ARG D 418 " ideal model delta sigma weight residual 111.30 98.74 12.56 2.30e+00 1.89e-01 2.98e+01 ... (remaining 28507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 11161 17.77 - 35.54: 1092 35.54 - 53.31: 203 53.31 - 71.08: 36 71.08 - 88.85: 16 Dihedral angle restraints: 12508 sinusoidal: 5020 harmonic: 7488 Sorted by residual: 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 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA HIS B 77 " pdb=" C HIS B 77 " pdb=" N PRO B 78 " pdb=" CA PRO B 78 " ideal model delta harmonic sigma weight residual -180.00 -157.46 -22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA HIS D 77 " pdb=" C HIS D 77 " pdb=" N PRO D 78 " pdb=" CA PRO D 78 " ideal model delta harmonic sigma weight residual -180.00 -157.46 -22.54 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 12505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2881 0.071 - 0.142: 228 0.142 - 0.213: 5 0.213 - 0.284: 3 0.284 - 0.355: 3 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA GLN B 417 " pdb=" N GLN B 417 " pdb=" C GLN B 417 " pdb=" CB GLN B 417 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA GLN A 417 " pdb=" N GLN A 417 " pdb=" C GLN A 417 " pdb=" CB GLN A 417 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA GLN D 417 " pdb=" N GLN D 417 " pdb=" C GLN D 417 " pdb=" CB GLN D 417 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 3117 not shown) Planarity restraints: 3644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 207 " 0.036 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO B 208 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 207 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO G 208 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO G 208 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 208 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 417 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C GLN B 417 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN B 417 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG B 418 " -0.012 2.00e-02 2.50e+03 ... (remaining 3641 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5217 2.79 - 3.32: 20446 3.32 - 3.85: 33262 3.85 - 4.37: 39351 4.37 - 4.90: 67309 Nonbonded interactions: 165585 Sorted by model distance: nonbonded pdb=" OE2 GLU B 71 " pdb=" OH TYR H 57 " model vdw 2.268 3.040 nonbonded pdb=" OE2 GLU D 71 " pdb=" OH TYR J 57 " model vdw 2.271 3.040 nonbonded pdb=" OE2 GLU G 71 " pdb=" OH TYR L 57 " model vdw 2.271 3.040 nonbonded pdb=" OE2 GLU A 71 " pdb=" OH TYR E 57 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR A 65 " pdb=" OH TYR A 99 " model vdw 2.280 3.040 ... (remaining 165580 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.710 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 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 0.038 21080 Z= 0.127 Angle : 0.617 12.558 28512 Z= 0.329 Chirality : 0.040 0.355 3120 Planarity : 0.003 0.056 3644 Dihedral : 14.673 88.848 7660 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.34 % Favored : 92.34 % Rotamer: Outliers : 0.14 % Allowed : 0.45 % Favored : 99.41 % Cbeta Deviations : 0.08 % 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: 0.02 (0.17), residues: 2492 helix: 1.16 (0.13), residues: 1584 sheet: -2.35 (0.54), residues: 40 loop : -2.08 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 142 TYR 0.009 0.001 TYR B 188 PHE 0.009 0.001 PHE D 493 TRP 0.011 0.001 TRP D 362 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00243 (21080) covalent geometry : angle 0.61693 (28512) hydrogen bonds : bond 0.21101 ( 1185) hydrogen bonds : angle 6.40135 ( 3462) *********************** 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 385 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 382 time to evaluate : 0.778 Fit side-chains REVERT: A 46 ASN cc_start: 0.8604 (t0) cc_final: 0.8117 (t0) REVERT: A 183 MET cc_start: 0.2445 (mmm) cc_final: 0.2057 (tpt) REVERT: A 429 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.6607 (mmt180) REVERT: B 46 ASN cc_start: 0.8600 (t0) cc_final: 0.8114 (t0) REVERT: B 183 MET cc_start: 0.2406 (mmm) cc_final: 0.2030 (tpt) REVERT: B 429 ARG cc_start: 0.7122 (ttm-80) cc_final: 0.6631 (mmt90) REVERT: D 46 ASN cc_start: 0.8600 (t0) cc_final: 0.8116 (t0) REVERT: D 183 MET cc_start: 0.2480 (mmm) cc_final: 0.2069 (tpt) REVERT: D 429 ARG cc_start: 0.7115 (ttm-80) cc_final: 0.6620 (mmt90) REVERT: G 46 ASN cc_start: 0.8595 (t0) cc_final: 0.8110 (t0) REVERT: G 183 MET cc_start: 0.2419 (mmm) cc_final: 0.2009 (tpt) REVERT: G 299 ARG cc_start: 0.7114 (ptp-170) cc_final: 0.6872 (mtt180) REVERT: G 429 ARG cc_start: 0.7120 (ttm-80) cc_final: 0.6603 (mmt90) REVERT: E 109 GLU cc_start: 0.7339 (mp0) cc_final: 0.7100 (mp0) REVERT: H 109 GLU cc_start: 0.7243 (mp0) cc_final: 0.7035 (mp0) REVERT: H 168 GLU cc_start: 0.7337 (tm-30) cc_final: 0.7130 (tm-30) REVERT: J 109 GLU cc_start: 0.7259 (mp0) cc_final: 0.7046 (mp0) REVERT: J 210 GLN cc_start: 0.7415 (mp10) cc_final: 0.7209 (mp10) REVERT: L 109 GLU cc_start: 0.7335 (mp0) cc_final: 0.7088 (mp0) REVERT: L 168 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7166 (tm-30) outliers start: 3 outliers final: 0 residues processed: 382 average time/residue: 0.1527 time to fit residues: 89.1781 Evaluate side-chains 294 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 144 ASN E 210 GLN H 210 GLN H 213 GLN J 210 GLN L 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.213267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.193903 restraints weight = 22193.023| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 0.83 r_work: 0.3913 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3868 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work: 0.3783 rms_B_bonded: 3.48 restraints_weight: 0.1250 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21080 Z= 0.209 Angle : 0.634 7.415 28512 Z= 0.332 Chirality : 0.044 0.161 3120 Planarity : 0.005 0.060 3644 Dihedral : 4.264 20.976 2804 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.50 % Favored : 92.34 % Rotamer: Outliers : 1.13 % Allowed : 7.32 % Favored : 91.55 % 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: 0.15 (0.17), residues: 2492 helix: 1.21 (0.13), residues: 1628 sheet: -0.90 (0.75), residues: 40 loop : -2.17 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 142 TYR 0.013 0.002 TYR A 188 PHE 0.018 0.002 PHE G 122 TRP 0.012 0.002 TRP A 362 HIS 0.006 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00489 (21080) covalent geometry : angle 0.63370 (28512) hydrogen bonds : bond 0.04612 ( 1185) hydrogen bonds : angle 4.51999 ( 3462) *********************** 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 327 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 302 time to evaluate : 0.685 Fit side-chains REVERT: A 42 LEU cc_start: 0.9042 (pt) cc_final: 0.8804 (pt) REVERT: A 429 ARG cc_start: 0.7324 (ttm-80) cc_final: 0.6998 (mmt180) REVERT: A 475 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: B 42 LEU cc_start: 0.9037 (pt) cc_final: 0.8800 (pt) REVERT: B 429 ARG cc_start: 0.7280 (ttm-80) cc_final: 0.6984 (mmt180) REVERT: B 475 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: D 42 LEU cc_start: 0.9043 (pt) cc_final: 0.8804 (pt) REVERT: D 429 ARG cc_start: 0.7312 (ttm-80) cc_final: 0.7015 (mmt180) REVERT: D 475 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: G 42 LEU cc_start: 0.9039 (pt) cc_final: 0.8802 (pt) REVERT: G 429 ARG cc_start: 0.7242 (ttm-80) cc_final: 0.6904 (mmt180) REVERT: G 475 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: E 109 GLU cc_start: 0.7955 (mp0) cc_final: 0.7716 (mp0) REVERT: H 109 GLU cc_start: 0.7965 (mp0) cc_final: 0.7681 (mp0) REVERT: J 109 GLU cc_start: 0.7978 (mp0) cc_final: 0.7695 (mp0) REVERT: L 109 GLU cc_start: 0.7928 (mp0) cc_final: 0.7694 (mp0) outliers start: 25 outliers final: 12 residues processed: 322 average time/residue: 0.1654 time to fit residues: 78.3503 Evaluate side-chains 285 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 269 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 221 CYS 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 J residue 66 SER Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 249 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS D 144 ASN G 414 HIS J 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.215381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.195668 restraints weight = 22269.236| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 0.85 r_work: 0.3875 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.3699 rms_B_bonded: 4.50 restraints_weight: 0.1250 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21080 Z= 0.154 Angle : 0.556 7.104 28512 Z= 0.294 Chirality : 0.041 0.160 3120 Planarity : 0.004 0.057 3644 Dihedral : 4.188 19.126 2804 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.26 % Favored : 92.58 % Rotamer: Outliers : 1.08 % Allowed : 10.99 % Favored : 87.93 % 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: 0.34 (0.17), residues: 2492 helix: 1.44 (0.13), residues: 1616 sheet: -0.86 (0.74), residues: 40 loop : -2.24 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 296 TYR 0.014 0.001 TYR G 188 PHE 0.022 0.002 PHE H 131 TRP 0.010 0.001 TRP D 362 HIS 0.004 0.001 HIS G 94 Details of bonding type rmsd covalent geometry : bond 0.00360 (21080) covalent geometry : angle 0.55593 (28512) hydrogen bonds : bond 0.04223 ( 1185) hydrogen bonds : angle 4.28008 ( 3462) *********************** 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 313 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 289 time to evaluate : 0.759 Fit side-chains REVERT: A 183 MET cc_start: 0.3065 (mmp) cc_final: 0.1971 (tpt) REVERT: A 429 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.7147 (mmt180) REVERT: A 475 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: B 183 MET cc_start: 0.3040 (mmp) cc_final: 0.1951 (tpt) REVERT: B 475 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: D 183 MET cc_start: 0.3025 (mmp) cc_final: 0.1947 (tpt) REVERT: D 475 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7790 (mt-10) REVERT: G 183 MET cc_start: 0.3025 (mmp) cc_final: 0.1958 (tpt) REVERT: G 475 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: E 109 GLU cc_start: 0.8031 (mp0) cc_final: 0.7827 (mp0) REVERT: J 109 GLU cc_start: 0.8054 (mp0) cc_final: 0.7845 (mp0) outliers start: 24 outliers final: 11 residues processed: 306 average time/residue: 0.1558 time to fit residues: 72.2274 Evaluate side-chains 286 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 271 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain G residue 393 SER 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 J residue 106 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 106 VAL 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: 0.5980 chunk 241 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 140 optimal weight: 0.0060 chunk 64 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 245 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 overall best weight: 3.1202 ------------------------------------------------------------------------------- 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 ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.209467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.187754 restraints weight = 22447.671| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 0.97 r_work: 0.3775 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21080 Z= 0.227 Angle : 0.628 8.193 28512 Z= 0.325 Chirality : 0.044 0.188 3120 Planarity : 0.005 0.055 3644 Dihedral : 4.456 19.291 2804 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.87 % Favored : 91.97 % Rotamer: Outliers : 1.27 % Allowed : 13.11 % Favored : 85.62 % 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: 0.22 (0.17), residues: 2492 helix: 1.26 (0.13), residues: 1656 sheet: -0.51 (0.79), residues: 40 loop : -2.27 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 61 TYR 0.016 0.002 TYR G 188 PHE 0.023 0.002 PHE E 131 TRP 0.010 0.002 TRP A 362 HIS 0.006 0.001 HIS D 491 Details of bonding type rmsd covalent geometry : bond 0.00549 (21080) covalent geometry : angle 0.62753 (28512) hydrogen bonds : bond 0.04392 ( 1185) hydrogen bonds : angle 4.29561 ( 3462) *********************** 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 311 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 283 time to evaluate : 0.672 Fit side-chains REVERT: A 183 MET cc_start: 0.2859 (mmp) cc_final: 0.1514 (tpt) REVERT: A 429 ARG cc_start: 0.7336 (ttm-80) cc_final: 0.7096 (mmt180) REVERT: A 475 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: B 183 MET cc_start: 0.2869 (mmp) cc_final: 0.1527 (tpt) REVERT: B 475 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: D 183 MET cc_start: 0.2912 (mmp) cc_final: 0.1568 (tpt) REVERT: D 475 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: G 183 MET cc_start: 0.2892 (mmp) cc_final: 0.1576 (tpt) REVERT: G 475 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: E 109 GLU cc_start: 0.7724 (mp0) cc_final: 0.7522 (mp0) outliers start: 28 outliers final: 17 residues processed: 302 average time/residue: 0.1479 time to fit residues: 68.6224 Evaluate side-chains 286 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain J residue 64 CYS Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 103 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 140 optimal weight: 0.0980 chunk 207 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 414 HIS E 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.213159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.190854 restraints weight = 22377.061| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 0.94 r_work: 0.3809 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work: 0.3632 rms_B_bonded: 4.56 restraints_weight: 0.1250 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21080 Z= 0.114 Angle : 0.533 8.874 28512 Z= 0.281 Chirality : 0.040 0.170 3120 Planarity : 0.004 0.054 3644 Dihedral : 4.219 16.863 2804 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.78 % Favored : 93.06 % Rotamer: Outliers : 1.40 % Allowed : 13.16 % Favored : 85.44 % 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: 0.53 (0.17), residues: 2492 helix: 1.57 (0.13), residues: 1628 sheet: -0.12 (0.82), residues: 40 loop : -2.24 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 296 TYR 0.014 0.001 TYR G 188 PHE 0.025 0.002 PHE J 131 TRP 0.010 0.001 TRP A 362 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00248 (21080) covalent geometry : angle 0.53326 (28512) hydrogen bonds : bond 0.03608 ( 1185) hydrogen bonds : angle 4.05096 ( 3462) *********************** 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 316 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 183 MET cc_start: 0.2898 (mmp) cc_final: 0.1681 (tpt) REVERT: A 429 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.6994 (mmt180) REVERT: A 475 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: B 183 MET cc_start: 0.2885 (mmp) cc_final: 0.1592 (tpt) REVERT: B 475 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: D 183 MET cc_start: 0.2917 (mmp) cc_final: 0.1612 (tpt) REVERT: D 475 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: G 183 MET cc_start: 0.2904 (mmp) cc_final: 0.1620 (tpt) REVERT: G 475 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: E 109 GLU cc_start: 0.8048 (mp0) cc_final: 0.7834 (mp0) REVERT: E 179 PHE cc_start: 0.7718 (m-10) cc_final: 0.7507 (m-10) REVERT: J 179 PHE cc_start: 0.7762 (m-10) cc_final: 0.7555 (m-10) REVERT: L 179 PHE cc_start: 0.7755 (m-10) cc_final: 0.7544 (m-10) outliers start: 31 outliers final: 11 residues processed: 312 average time/residue: 0.1497 time to fit residues: 71.6230 Evaluate side-chains 290 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 275 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 300 ILE 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 G residue 490 ASN Chi-restraints excluded: chain E residue 64 CYS 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 64 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 211 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 150 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN D 425 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.215587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.197977 restraints weight = 22081.711| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 0.70 r_work: 0.3808 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work: 0.3644 rms_B_bonded: 3.33 restraints_weight: 0.1250 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21080 Z= 0.138 Angle : 0.543 10.949 28512 Z= 0.283 Chirality : 0.040 0.146 3120 Planarity : 0.004 0.053 3644 Dihedral : 4.170 16.038 2804 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.34 % Favored : 92.50 % Rotamer: Outliers : 1.13 % Allowed : 14.01 % Favored : 84.86 % 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: 0.61 (0.17), residues: 2492 helix: 1.58 (0.13), residues: 1648 sheet: -0.36 (0.77), residues: 40 loop : -2.14 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.017 0.001 TYR B 134 PHE 0.030 0.002 PHE H 178 TRP 0.009 0.001 TRP G 362 HIS 0.004 0.001 HIS G 94 Details of bonding type rmsd covalent geometry : bond 0.00319 (21080) covalent geometry : angle 0.54288 (28512) hydrogen bonds : bond 0.03660 ( 1185) hydrogen bonds : angle 4.01884 ( 3462) *********************** 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 306 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 281 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 429 ARG cc_start: 0.7213 (ttm-80) cc_final: 0.6897 (mmt180) REVERT: A 475 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: B 475 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: D 475 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: G 183 MET cc_start: 0.2942 (mmp) cc_final: 0.1633 (tpt) REVERT: G 475 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: E 109 GLU cc_start: 0.7841 (mp0) cc_final: 0.7629 (mp0) outliers start: 25 outliers final: 17 residues processed: 300 average time/residue: 0.1487 time to fit residues: 68.7236 Evaluate side-chains 295 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 274 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 A residue 490 ASN Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain G residue 490 ASN Chi-restraints excluded: chain E residue 64 CYS 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 64 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 229 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 191 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.209304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.186733 restraints weight = 22235.636| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 0.97 r_work: 0.3762 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21080 Z= 0.197 Angle : 0.606 11.266 28512 Z= 0.312 Chirality : 0.043 0.198 3120 Planarity : 0.004 0.051 3644 Dihedral : 4.342 16.824 2804 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.42 % Favored : 92.42 % Rotamer: Outliers : 1.40 % Allowed : 15.19 % Favored : 83.41 % 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: 0.46 (0.17), residues: 2492 helix: 1.43 (0.13), residues: 1668 sheet: -0.49 (0.75), residues: 40 loop : -2.21 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 61 TYR 0.016 0.001 TYR G 188 PHE 0.026 0.002 PHE E 178 TRP 0.009 0.001 TRP G 362 HIS 0.004 0.001 HIS B 491 Details of bonding type rmsd covalent geometry : bond 0.00475 (21080) covalent geometry : angle 0.60595 (28512) hydrogen bonds : bond 0.04031 ( 1185) hydrogen bonds : angle 4.13212 ( 3462) *********************** 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 302 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 271 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 183 MET cc_start: 0.2749 (mmp) cc_final: 0.1531 (tpt) REVERT: A 204 VAL cc_start: 0.7944 (m) cc_final: 0.7744 (t) REVERT: A 429 ARG cc_start: 0.7303 (ttm-80) cc_final: 0.6996 (mmt180) REVERT: A 475 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: B 183 MET cc_start: 0.2642 (mmp) cc_final: 0.1414 (tpt) REVERT: B 475 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: D 183 MET cc_start: 0.2758 (mmp) cc_final: 0.1523 (tpt) REVERT: D 475 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: G 183 MET cc_start: 0.2802 (mmp) cc_final: 0.1370 (tpt) REVERT: G 475 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: E 109 GLU cc_start: 0.7772 (mp0) cc_final: 0.7539 (mp0) REVERT: H 208 SER cc_start: 0.8788 (m) cc_final: 0.8472 (m) outliers start: 31 outliers final: 19 residues processed: 291 average time/residue: 0.1547 time to fit residues: 70.2891 Evaluate side-chains 288 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 265 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 A residue 490 ASN Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain G residue 490 ASN Chi-restraints excluded: chain E residue 64 CYS 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 64 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.211776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.190308 restraints weight = 22274.413| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 0.97 r_work: 0.3688 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work: 0.3520 rms_B_bonded: 4.05 restraints_weight: 0.1250 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21080 Z= 0.122 Angle : 0.548 11.757 28512 Z= 0.284 Chirality : 0.040 0.165 3120 Planarity : 0.004 0.052 3644 Dihedral : 4.154 16.688 2804 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.34 % Favored : 92.50 % Rotamer: Outliers : 1.27 % Allowed : 15.82 % Favored : 82.91 % 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: 0.66 (0.17), residues: 2492 helix: 1.72 (0.13), residues: 1624 sheet: -0.41 (0.76), residues: 40 loop : -2.26 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.014 0.001 TYR G 188 PHE 0.032 0.002 PHE J 131 TRP 0.010 0.001 TRP A 362 HIS 0.004 0.001 HIS G 94 Details of bonding type rmsd covalent geometry : bond 0.00276 (21080) covalent geometry : angle 0.54832 (28512) hydrogen bonds : bond 0.03476 ( 1185) hydrogen bonds : angle 3.93955 ( 3462) *********************** 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 305 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 183 MET cc_start: 0.2687 (mmp) cc_final: 0.1327 (tpt) REVERT: A 204 VAL cc_start: 0.7819 (m) cc_final: 0.7576 (t) REVERT: A 429 ARG cc_start: 0.7237 (ttm-80) cc_final: 0.6948 (mmt180) REVERT: A 475 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: B 183 MET cc_start: 0.2677 (mmp) cc_final: 0.1298 (tpt) REVERT: B 475 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: D 183 MET cc_start: 0.2678 (mmp) cc_final: 0.1324 (tpt) REVERT: D 475 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: G 183 MET cc_start: 0.2888 (mmp) cc_final: 0.1442 (tpt) REVERT: G 204 VAL cc_start: 0.7937 (m) cc_final: 0.7689 (t) REVERT: G 475 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7906 (mt-10) outliers start: 28 outliers final: 16 residues processed: 301 average time/residue: 0.1455 time to fit residues: 68.0966 Evaluate side-chains 287 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 267 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 393 SER 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 G residue 490 ASN Chi-restraints excluded: chain E residue 64 CYS 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 64 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 225 optimal weight: 0.3980 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 238 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.210307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.184205 restraints weight = 22232.395| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.15 r_work: 0.3758 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21080 Z= 0.154 Angle : 0.576 11.738 28512 Z= 0.295 Chirality : 0.041 0.160 3120 Planarity : 0.004 0.052 3644 Dihedral : 4.188 16.316 2804 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.14 % Favored : 92.70 % Rotamer: Outliers : 1.04 % Allowed : 16.68 % Favored : 82.28 % 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: 0.62 (0.17), residues: 2492 helix: 1.58 (0.13), residues: 1664 sheet: -0.52 (0.73), residues: 40 loop : -2.19 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 296 TYR 0.022 0.001 TYR A 134 PHE 0.026 0.002 PHE J 131 TRP 0.010 0.001 TRP A 362 HIS 0.004 0.001 HIS G 94 Details of bonding type rmsd covalent geometry : bond 0.00362 (21080) covalent geometry : angle 0.57579 (28512) hydrogen bonds : bond 0.03664 ( 1185) hydrogen bonds : angle 3.97426 ( 3462) *********************** 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 296 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 273 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 183 MET cc_start: 0.2318 (mmp) cc_final: 0.1055 (tpt) REVERT: A 204 VAL cc_start: 0.7751 (m) cc_final: 0.7551 (t) REVERT: A 429 ARG cc_start: 0.7259 (ttm-80) cc_final: 0.7017 (mmt180) REVERT: A 475 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: B 183 MET cc_start: 0.2386 (mmp) cc_final: 0.1100 (tpt) REVERT: B 475 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: D 183 MET cc_start: 0.2393 (mmp) cc_final: 0.1118 (tpt) REVERT: D 475 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: G 183 MET cc_start: 0.2627 (mmp) cc_final: 0.1237 (tpt) REVERT: G 204 VAL cc_start: 0.7752 (m) cc_final: 0.7509 (t) REVERT: G 475 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7812 (mt-10) outliers start: 23 outliers final: 18 residues processed: 291 average time/residue: 0.1459 time to fit residues: 66.0340 Evaluate side-chains 291 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 269 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 393 SER 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 G residue 490 ASN Chi-restraints excluded: chain E residue 64 CYS 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 64 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 158 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.208993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.180929 restraints weight = 22302.104| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.26 r_work: 0.3717 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21080 Z= 0.184 Angle : 0.622 14.368 28512 Z= 0.315 Chirality : 0.042 0.158 3120 Planarity : 0.004 0.051 3644 Dihedral : 4.322 16.843 2804 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.46 % Favored : 92.38 % Rotamer: Outliers : 1.18 % Allowed : 16.95 % Favored : 81.87 % 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: 0.50 (0.17), residues: 2492 helix: 1.49 (0.13), residues: 1664 sheet: -0.54 (0.72), residues: 40 loop : -2.25 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 296 TYR 0.017 0.001 TYR G 188 PHE 0.025 0.002 PHE J 131 TRP 0.009 0.001 TRP D 362 HIS 0.004 0.001 HIS G 94 Details of bonding type rmsd covalent geometry : bond 0.00441 (21080) covalent geometry : angle 0.62150 (28512) hydrogen bonds : bond 0.03913 ( 1185) hydrogen bonds : angle 4.05797 ( 3462) ********************** 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 295 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 183 MET cc_start: 0.2312 (mmp) cc_final: 0.1029 (tpt) REVERT: A 429 ARG cc_start: 0.7330 (ttm-80) cc_final: 0.7073 (mmt180) REVERT: A 475 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: B 183 MET cc_start: 0.2364 (mmp) cc_final: 0.1059 (tpt) REVERT: B 475 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: D 183 MET cc_start: 0.2360 (mmp) cc_final: 0.1086 (tpt) REVERT: D 475 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: G 183 MET cc_start: 0.2460 (mmp) cc_final: 0.1003 (tpt) REVERT: G 475 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7851 (mt-10) outliers start: 26 outliers final: 21 residues processed: 289 average time/residue: 0.1510 time to fit residues: 67.3345 Evaluate side-chains 290 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain G residue 490 ASN Chi-restraints excluded: chain E residue 64 CYS 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 64 CYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain L residue 64 CYS Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 2 optimal weight: 0.4980 chunk 141 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.209476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.181675 restraints weight = 22274.817| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.17 r_work: 0.3677 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21080 Z= 0.155 Angle : 0.594 12.395 28512 Z= 0.302 Chirality : 0.041 0.150 3120 Planarity : 0.004 0.052 3644 Dihedral : 4.256 16.499 2804 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.90 % Favored : 92.94 % Rotamer: Outliers : 1.18 % Allowed : 17.09 % Favored : 81.74 % 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: 0.54 (0.17), residues: 2492 helix: 1.54 (0.13), residues: 1664 sheet: -0.39 (0.73), residues: 40 loop : -2.28 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 296 TYR 0.016 0.001 TYR G 188 PHE 0.025 0.002 PHE J 131 TRP 0.010 0.001 TRP D 362 HIS 0.004 0.001 HIS G 94 Details of bonding type rmsd covalent geometry : bond 0.00364 (21080) covalent geometry : angle 0.59442 (28512) hydrogen bonds : bond 0.03706 ( 1185) hydrogen bonds : angle 3.99422 ( 3462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5331.29 seconds wall clock time: 92 minutes 6.46 seconds (5526.46 seconds total)